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<p><strong>Last updated:</strong> 2019-01-16</p>
<strong>workflowr checks:</strong> <small>(Click a bullet for more information)</small>
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<p><details> <summary> <strong style="color:blue;">✔</strong> <strong>R Markdown file:</strong> up-to-date </summary></p>
<p>Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.</p>
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<p><details> <summary> <strong style="color:blue;">✔</strong> <strong>Repository version:</strong> <a href="https://github.com/brimittleman/threeprimeseq/tree/6aa94e46191d361cdb422647f48195789fdcf789" target="_blank">6aa94e4</a> </summary></p>
Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility. The version displayed above was the version of the Git repository at the time these results were generated. <br><br> Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use <code>wflow_publish</code> or <code>wflow_git_commit</code>). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:
<pre><code>
Ignored files:
    Ignored:    .DS_Store
    Ignored:    .Rhistory
    Ignored:    .Rproj.user/
    Ignored:    data/.DS_Store
    Ignored:    output/.DS_Store

Untracked files:
    Untracked:  KalistoAbundance18486.txt
    Untracked:  analysis/DirectionapaQTL.Rmd
    Untracked:  analysis/EvaleQTLs.Rmd
    Untracked:  analysis/PreAshExplore.Rmd
    Untracked:  analysis/YL_QTL_test.Rmd
    Untracked:  analysis/ncbiRefSeq_sm.sort.mRNA.bed
    Untracked:  analysis/snake.config.notes.Rmd
    Untracked:  analysis/verifyBAM.Rmd
    Untracked:  code/PeaksToCoverPerReads.py
    Untracked:  code/strober_pc_pve_heatmap_func.R
    Untracked:  data/18486.genecov.txt
    Untracked:  data/APApeaksYL.total.inbrain.bed
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    Untracked:  data/YL-SP-18486-T_S9_R1_001-genecov.txt
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Unstaged changes:
    Modified:   analysis/28ind.peak.explore.Rmd
    Modified:   analysis/CompareLianoglouData.Rmd
    Modified:   analysis/NewPeakPostMP.Rmd
    Modified:   analysis/apaQTLoverlapGWAS.Rmd
    Modified:   analysis/cleanupdtseq.internalpriming.Rmd
    Modified:   analysis/coloc_apaQTLs_protQTLs.Rmd
    Modified:   analysis/dif.iso.usage.leafcutter.Rmd
    Modified:   analysis/diff_iso_pipeline.Rmd
    Modified:   analysis/explainpQTLs.Rmd
    Modified:   analysis/explore.filters.Rmd
    Modified:   analysis/flash2mash.Rmd
    Modified:   analysis/mispriming_approach.Rmd
    Modified:   analysis/overlapMolQTL.Rmd
    Modified:   analysis/overlapMolQTL.opposite.Rmd
    Modified:   analysis/overlap_qtls.Rmd
    Modified:   analysis/peakOverlap_oppstrand.Rmd
    Modified:   analysis/pheno.leaf.comb.Rmd
    Modified:   analysis/swarmPlots_QTLs.Rmd
    Modified:   analysis/test.max2.Rmd
    Modified:   analysis/understandPeaks.Rmd
    Modified:   code/Snakefile

</code></pre>
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2018-11-15
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<td style="text-align:left;">
fix gwas bullet
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/brimittleman/threeprimeseq/24821f2e800b26456114ff1400996f16ebbaff3d/docs/index.html" target="_blank">24821f2</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-11-12
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/brimittleman/threeprimeseq/2ec5ffd37187beac4a5124fbb700b2ea52a1e75a/docs/index.html" target="_blank">2ec5ffd</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-11-07
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
Rmd
</td>
<td style="text-align:left;">
<a href="https://github.com/brimittleman/threeprimeseq/blob/962e39bcfc173365546499232b60d586f6470f38/analysis/index.Rmd" target="_blank">962e39b</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-11-07
</td>
<td style="text-align:left;">
move chromhmm analysis to its own analysis
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/brimittleman/threeprimeseq/3de08482d4164845cac29ac8b3fccc3d0a8e2eea/docs/index.html" target="_blank">3de0848</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-11-06
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
Rmd
</td>
<td style="text-align:left;">
<a href="https://github.com/brimittleman/threeprimeseq/blob/b5f744f599ad5ec725eb3e31b86e804979f568b2/analysis/index.Rmd" target="_blank">b5f744f</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-11-06
</td>
<td style="text-align:left;">
initiate flash2mash
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/brimittleman/threeprimeseq/d01545f42315390a1a4fdac3f228b11a78b5e403/docs/index.html" target="_blank">d01545f</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-10-30
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
Rmd
</td>
<td style="text-align:left;">
<a href="https://github.com/brimittleman/threeprimeseq/blob/9c9486dfcd74721fe66d7e3a0eee0f51fef2566a/analysis/index.Rmd" target="_blank">9c9486d</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-10-30
</td>
<td style="text-align:left;">
add genoem tracks code
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/brimittleman/threeprimeseq/0428c8cc7dbe48e523ec661d5a0215e784135d7b/docs/index.html" target="_blank">0428c8c</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-10-29
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
Rmd
</td>
<td style="text-align:left;">
<a href="https://github.com/brimittleman/threeprimeseq/blob/42d0e3d7c7875581d9b5bd1d63dc658b03e21f11/analysis/index.Rmd" target="_blank">42d0e3d</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-10-29
</td>
<td style="text-align:left;">
add gwas overlap to index
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/brimittleman/threeprimeseq/de860f0e5f84639460e9157c55f0024274bfb7d4/docs/index.html" target="_blank">de860f0</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-10-24
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
Rmd
</td>
<td style="text-align:left;">
<a href="https://github.com/brimittleman/threeprimeseq/blob/96a97f4b407baa2e87100144f096a2a9c483e874/analysis/index.Rmd" target="_blank">96a97f4</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-10-24
</td>
<td style="text-align:left;">
add nuclear characterization
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/brimittleman/threeprimeseq/5649809b5974649e2d31ecf7dc6441beb7e28081/docs/index.html" target="_blank">5649809</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-10-22
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
Rmd
</td>
<td style="text-align:left;">
<a href="https://github.com/brimittleman/threeprimeseq/blob/c8dbaf06efdfed0b7563c03c01ccc390b6cea6c0/analysis/index.Rmd" target="_blank">c8dbaf0</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-10-22
</td>
<td style="text-align:left;">
add apa prot rna overlap
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/brimittleman/threeprimeseq/eb02fbc3fdca9d239eeba2bac84bd1a4d20dc434/docs/index.html" target="_blank">eb02fbc</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-10-11
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
Rmd
</td>
<td style="text-align:left;">
<a href="https://github.com/brimittleman/threeprimeseq/blob/f819c8e3a4ef75111646f1ca1e8343711c4133f3/analysis/index.Rmd" target="_blank">f819c8e</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-10-11
</td>
<td style="text-align:left;">
add distance metric analsis total apaQTL
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/brimittleman/threeprimeseq/a7e5fa22643969bcb59ea9f7ab3696f6b82430d9/docs/index.html" target="_blank">a7e5fa2</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-10-11
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
Rmd
</td>
<td style="text-align:left;">
<a href="https://github.com/brimittleman/threeprimeseq/blob/1e7fbbb20e4aadbe860965f014b2aa62b19fe821/analysis/index.Rmd" target="_blank">1e7fbbb</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-10-11
</td>
<td style="text-align:left;">
update format
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/brimittleman/threeprimeseq/729c084f3118cae3ba8e7adde5c23797025f43ff/docs/index.html" target="_blank">729c084</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-10-11
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
Rmd
</td>
<td style="text-align:left;">
<a href="https://github.com/brimittleman/threeprimeseq/blob/89f119a4d395b475d4f3e663f1509fb0b372b973/analysis/index.Rmd" target="_blank">89f119a</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-10-11
</td>
<td style="text-align:left;">
update format
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/brimittleman/threeprimeseq/22aa0872ec0621164f376f8225f985be6112e20f/docs/index.html" target="_blank">22aa087</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-10-08
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
Rmd
</td>
<td style="text-align:left;">
<a href="https://github.com/brimittleman/threeprimeseq/blob/11f9dfa2e7e97a7279afc91e4f1a8f2cdb1f856e/analysis/index.Rmd" target="_blank">11f9dfa</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-10-08
</td>
<td style="text-align:left;">
overlap molQTL opp dir
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/brimittleman/threeprimeseq/077ed603f855c9fd95c9e77bb1008695e8ba3891/docs/index.html" target="_blank">077ed60</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-10-08
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/brimittleman/threeprimeseq/7369f8ebf5a521bb3cd265f35ae26915f39b5bee/docs/index.html" target="_blank">7369f8e</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-10-02
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
Rmd
</td>
<td style="text-align:left;">
<a href="https://github.com/brimittleman/threeprimeseq/blob/f66679bc1d71db8c924eba94a35f4643d179ae7e/analysis/index.Rmd" target="_blank">f66679b</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-10-02
</td>
<td style="text-align:left;">
overlap plots at peak level
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/brimittleman/threeprimeseq/2e0d959a51368bcfa9ebc00b54b6b86195e8835a/docs/index.html" target="_blank">2e0d959</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-10-01
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
Rmd
</td>
<td style="text-align:left;">
<a href="https://github.com/brimittleman/threeprimeseq/blob/9d6ee033c3a681f38437f2a0cee61cef97ac51da/analysis/index.Rmd" target="_blank">9d6ee03</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-10-01
</td>
<td style="text-align:left;">
add 4su plots
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/brimittleman/threeprimeseq/da0f70ef6a8662ab8ac9ee900915ed61e2e31fd6/docs/index.html" target="_blank">da0f70e</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-10-01
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
Rmd
</td>
<td style="text-align:left;">
<a href="https://github.com/brimittleman/threeprimeseq/blob/fecb046a72c0ed7df318d9642fa62e4c7af56cd8/analysis/index.Rmd" target="_blank">fecb046</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-10-01
</td>
<td style="text-align:left;">
fix overlapfile
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/brimittleman/threeprimeseq/ac983db135c4ca1872cc58b4efea050275858722/docs/index.html" target="_blank">ac983db</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-10-01
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
Rmd
</td>
<td style="text-align:left;">
<a href="https://github.com/brimittleman/threeprimeseq/blob/35142fb308209cce516f74504f2f1a3abcfdff51/analysis/index.Rmd" target="_blank">35142fb</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-10-01
</td>
<td style="text-align:left;">
overlap QTL plots
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/brimittleman/threeprimeseq/149d033c96899a702b4c0a7320484cb980e3fb56/docs/index.html" target="_blank">149d033</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-09-26
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/brimittleman/threeprimeseq/aaed5fd02287453b28ab53c96adb5d51b5c385dd/docs/index.html" target="_blank">aaed5fd</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-09-26
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
Rmd
</td>
<td style="text-align:left;">
<a href="https://github.com/brimittleman/threeprimeseq/blob/eda266ec447da55ce6a5e62e907e634cbc547a20/analysis/index.Rmd" target="_blank">eda266e</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-09-26
</td>
<td style="text-align:left;">
test peak to gene transcript dist
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/brimittleman/threeprimeseq/47cd4bf7e1f277a76f2c44c6869c62f2211868e9/docs/index.html" target="_blank">47cd4bf</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-09-26
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/brimittleman/threeprimeseq/b1bcf9916b400de7a1ae40bb2335c8ef064c9048/docs/index.html" target="_blank">b1bcf99</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-09-25
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/brimittleman/threeprimeseq/d3bb2874e82a9160c3a68644ff092be0c8d799d1/docs/index.html" target="_blank">d3bb287</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-09-24
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
Rmd
</td>
<td style="text-align:left;">
<a href="https://github.com/brimittleman/threeprimeseq/blob/f7934ce5afa448c50043b68c5920186b0c66f460/analysis/index.Rmd" target="_blank">f7934ce</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-09-24
</td>
<td style="text-align:left;">
wflow_publish(c(“index.Rmd”, “39indQC.Rmd”))
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/brimittleman/threeprimeseq/f92a58fb8dd5bf15e528a9d1762e34ae3c25e005/docs/index.html" target="_blank">f92a58f</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-09-06
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
Rmd
</td>
<td style="text-align:left;">
<a href="https://github.com/brimittleman/threeprimeseq/blob/46b7343493337a9c20b5ce490b66cbb942467169/analysis/index.Rmd" target="_blank">46b7343</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-09-06
</td>
<td style="text-align:left;">
add overlap analysis with code to subset
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/brimittleman/threeprimeseq/b4bda1b4c6cb9cd811f4133bca3184c00583c706/docs/index.html" target="_blank">b4bda1b</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-08-30
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/brimittleman/threeprimeseq/e000583e8d094de80cd8cb12bc6cb3933f15a645/docs/index.html" target="_blank">e000583</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-08-30
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
Rmd
</td>
<td style="text-align:left;">
<a href="https://github.com/brimittleman/threeprimeseq/blob/a5f527674983b1420a3c82e09ac39e69218d690b/analysis/index.Rmd" target="_blank">a5f5276</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-08-30
</td>
<td style="text-align:left;">
initialize diff iso pipeline
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/brimittleman/threeprimeseq/c6dc97bf8c0353ab9179b44a1f9ed8210f4c0adb/docs/index.html" target="_blank">c6dc97b</a>
</td>
<td style="text-align:left;">
brimittleman
</td>
<td style="text-align:left;">
2018-08-28
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/brimittleman/threeprimeseq/5564e259b7b24257b0d4e275873dafca7b024166/docs/index.html" target="_blank">5564e25</a>
</td>
<td style="text-align:left;">
brimittleman
</td>
<td style="text-align:left;">
2018-08-20
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
Rmd
</td>
<td style="text-align:left;">
<a href="https://github.com/brimittleman/threeprimeseq/blob/6b1b51c30cedc1bbdf21009104f126a8b4add401/analysis/index.Rmd" target="_blank">6b1b51c</a>
</td>
<td style="text-align:left;">
brimittleman
</td>
<td style="text-align:left;">
2018-08-20
</td>
<td style="text-align:left;">
start qtl analsis, add to index
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/brimittleman/threeprimeseq/c67380e570e74625b061e504b345fae77f0e3a6e/docs/index.html" target="_blank">c67380e</a>
</td>
<td style="text-align:left;">
brimittleman
</td>
<td style="text-align:left;">
2018-08-14
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/brimittleman/threeprimeseq/38bfbaf6b3e1b6f8e8fd397af1b86d34dd711a9e/docs/index.html" target="_blank">38bfbaf</a>
</td>
<td style="text-align:left;">
brimittleman
</td>
<td style="text-align:left;">
2018-08-09
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
Rmd
</td>
<td style="text-align:left;">
<a href="https://github.com/brimittleman/threeprimeseq/blob/03761cbbf00f95021204eefca436dbb1f2146cbc/analysis/index.Rmd" target="_blank">03761cb</a>
</td>
<td style="text-align:left;">
brimittleman
</td>
<td style="text-align:left;">
2018-08-09
</td>
<td style="text-align:left;">
start peak explore analysis for 54 libraries
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/brimittleman/threeprimeseq/e5a8da629657f8df6a23af081905e7dcab9fe98d/docs/index.html" target="_blank">e5a8da6</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-07-30
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
Rmd
</td>
<td style="text-align:left;">
<a href="https://github.com/brimittleman/threeprimeseq/blob/422a428cf40c5283c7dc0ba0d3cc21d8739cddb3/analysis/index.Rmd" target="_blank">422a428</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-07-30
</td>
<td style="text-align:left;">
add peak cove pipeline and combined lane qc
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/brimittleman/threeprimeseq/0398fdb061b51ffc376cca2a37bee74727674489/docs/index.html" target="_blank">0398fdb</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-07-25
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
Rmd
</td>
<td style="text-align:left;">
<a href="https://github.com/brimittleman/threeprimeseq/blob/2d41f11ceda8b51e78e2a040bc3ab99084c228a9/analysis/index.Rmd" target="_blank">2d41f11</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-07-25
</td>
<td style="text-align:left;">
add expand smash to index
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/brimittleman/threeprimeseq/3a5a8fe9a053a464ef64ed3c411bdedf82003927/docs/index.html" target="_blank">3a5a8fe</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-07-25
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/brimittleman/threeprimeseq/a34f9c17e0111475b79b8ba65678d7cd03ccf7e8/docs/index.html" target="_blank">a34f9c1</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-07-17
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
Rmd
</td>
<td style="text-align:left;">
<a href="https://github.com/brimittleman/threeprimeseq/blob/ca9cee943f269ffa18819efc8aa0ffa44f39f971/analysis/index.Rmd" target="_blank">ca9cee9</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-07-17
</td>
<td style="text-align:left;">
add smash test to index
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/brimittleman/threeprimeseq/c3ca148d27b4e58f712221b619052926fd20a50e/docs/index.html" target="_blank">c3ca148</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-07-17
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/brimittleman/threeprimeseq/dc4a51af1b101200e1685b760ac3f5c78db359b3/docs/index.html" target="_blank">dc4a51a</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-07-16
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
Rmd
</td>
<td style="text-align:left;">
<a href="https://github.com/brimittleman/threeprimeseq/blob/4fede8412f8277c95afc167709e9e370c386cf8b/analysis/index.Rmd" target="_blank">4fede84</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-07-16
</td>
<td style="text-align:left;">
add eval brain analysis
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/brimittleman/threeprimeseq/cfc8f437a3e2701980064f4423d8042c6144dd1d/docs/index.html" target="_blank">cfc8f43</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-07-13
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
Rmd
</td>
<td style="text-align:left;">
<a href="https://github.com/brimittleman/threeprimeseq/blob/4a847692c90977347c2a192e8e68e1d2d02b6fa5/analysis/index.Rmd" target="_blank">4a84769</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-07-13
</td>
<td style="text-align:left;">
add analysis for coparing coverage of RNAseq and 3’ seq
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/brimittleman/threeprimeseq/210cd2b1dff2619ce69c54368d8d332412aa1677/docs/index.html" target="_blank">210cd2b</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-07-05
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
Rmd
</td>
<td style="text-align:left;">
<a href="https://github.com/brimittleman/threeprimeseq/blob/8b622c3a9568a7f7f8c639b02a1da43563cebbd3/analysis/index.Rmd" target="_blank">8b622c3</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-07-05
</td>
<td style="text-align:left;">
add denovo to index
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/brimittleman/threeprimeseq/ee777df63592d6f252dd40a4cdc2c94baf53ffa9/docs/index.html" target="_blank">ee777df</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-06-26
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
Rmd
</td>
<td style="text-align:left;">
<a href="https://github.com/brimittleman/threeprimeseq/blob/789d8ef3fbeb727e66635f978480d6b768b290dd/analysis/index.Rmd" target="_blank">789d8ef</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-06-26
</td>
<td style="text-align:left;">
start test macs analysis. download package
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/brimittleman/threeprimeseq/30b415e3b95d62eafebb6a4824a29fba6c727be2/docs/index.html" target="_blank">30b415e</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-06-19
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/brimittleman/threeprimeseq/08b593457c104b333a203741789e2d632e85bfa1/docs/index.html" target="_blank">08b5934</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-06-13
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
Rmd
</td>
<td style="text-align:left;">
<a href="https://github.com/brimittleman/threeprimeseq/blob/642faf0176cbdb3b251de2e62b9f5dc9d385bbdf/analysis/index.Rmd" target="_blank">642faf0</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-06-13
</td>
<td style="text-align:left;">
start PAS enrichment analysis
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/brimittleman/threeprimeseq/4ef7d85554ed0db97548af29c6d994675af4837e/docs/index.html" target="_blank">4ef7d85</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-06-11
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
Rmd
</td>
<td style="text-align:left;">
<a href="https://github.com/brimittleman/threeprimeseq/blob/03c7b1448ea0c93a1d7a0b2d589e8ef964bf7bba/analysis/index.Rmd" target="_blank">03c7b14</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-06-11
</td>
<td style="text-align:left;">
start A analysis
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/brimittleman/threeprimeseq/062808d7f8f0132374041057f946a2c28c32797b/docs/index.html" target="_blank">062808d</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-06-07
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/brimittleman/threeprimeseq/86cfd9ff2fdd20c9bcc0f2872ca016b383d81700/docs/index.html" target="_blank">86cfd9f</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-06-06
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
Rmd
</td>
<td style="text-align:left;">
<a href="https://github.com/brimittleman/threeprimeseq/blob/a19683c3a42318377499f44fdd98f7af8ce4d2fd/analysis/index.Rmd" target="_blank">a19683c</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-06-06
</td>
<td style="text-align:left;">
start dif isoform analysis
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/brimittleman/threeprimeseq/710cf6a06e3904e99384341936f5c8b4a2a67428/docs/index.html" target="_blank">710cf6a</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-05-29
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
Rmd
</td>
<td style="text-align:left;">
<a href="https://github.com/brimittleman/threeprimeseq/blob/d58bc138fd71227816b58cffda2ccf2df7199808/analysis/index.Rmd" target="_blank">d58bc13</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-05-29
</td>
<td style="text-align:left;">
start 200 bp analysis
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/brimittleman/threeprimeseq/96ecbb125b7504e34275073c4369760db2ef8c3a/docs/index.html" target="_blank">96ecbb1</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-05-26
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
Rmd
</td>
<td style="text-align:left;">
<a href="https://github.com/brimittleman/threeprimeseq/blob/2076ce905888ca32e1fc086f15e954c7dde05450/analysis/index.Rmd" target="_blank">2076ce9</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-05-26
</td>
<td style="text-align:left;">
initial commit, gene level analysis
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/brimittleman/threeprimeseq/b5cdd59432005e3c407edeab96984f4d90c65b45/docs/index.html" target="_blank">b5cdd59</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-05-26
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
Rmd
</td>
<td style="text-align:left;">
<a href="https://github.com/brimittleman/threeprimeseq/blob/9a49459368772f030622712864c469ecee83a53a/analysis/index.Rmd" target="_blank">9a49459</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-05-26
</td>
<td style="text-align:left;">
start map qc analysis
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/brimittleman/threeprimeseq/924952b3c14f5a58131b1b99ae8be276d3b2d37f/docs/index.html" target="_blank">924952b</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-05-09
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
Rmd
</td>
<td style="text-align:left;">
<a href="https://github.com/brimittleman/threeprimeseq/blob/f8ce0fcfc549967f30ad08e19962c8135bb5dc27/analysis/index.Rmd" target="_blank">f8ce0fc</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-05-09
</td>
<td style="text-align:left;">
Update to 1.0
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/brimittleman/threeprimeseq/f8ce0fcfc549967f30ad08e19962c8135bb5dc27/docs/index.html" target="_blank">f8ce0fc</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-05-09
</td>
<td style="text-align:left;">
Update to 1.0
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/brimittleman/threeprimeseq/3dd80ef12a6e2e8ba83dc7987ec22d667d4b7492/docs/index.html" target="_blank">3dd80ef</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-05-08
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
Rmd
</td>
<td style="text-align:left;">
<a href="https://github.com/brimittleman/threeprimeseq/blob/519447d91969a0dc7db57d52cc61ecd71a9c53ab/analysis/index.Rmd" target="_blank">519447d</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-05-08
</td>
<td style="text-align:left;">
Add total.nuc.rnaseq analysis
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/brimittleman/threeprimeseq/889c9c6fa9085578dbb6d3e233c1ee787daef080/docs/index.html" target="_blank">889c9c6</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-05-02
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/brimittleman/threeprimeseq/9d196cf4b24ebee34e9624c46536a9c5aeca4f44/docs/index.html" target="_blank">9d196cf</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-05-02
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/brimittleman/threeprimeseq/972ef3effabfa330e5e75404d603f5ed2fb2f5df/docs/index.html" target="_blank">972ef3e</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-05-02
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
Rmd
</td>
<td style="text-align:left;">
<a href="https://github.com/brimittleman/threeprimeseq/blob/6cc5321541eca63223ad1bd790071d38ebb5bd7d/analysis/index.Rmd" target="_blank">6cc5321</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-05-02
</td>
<td style="text-align:left;">
add home page information
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/brimittleman/threeprimeseq/e12dd6cde00d646f994e07a4b5bd67138ad08494/docs/index.html" target="_blank">e12dd6c</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-05-01
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
Rmd
</td>
<td style="text-align:left;">
<a href="https://github.com/brimittleman/threeprimeseq/blob/0e95115337380d333adf3ee43adceea878e04ff8/analysis/index.Rmd" target="_blank">0e95115</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-05-01
</td>
<td style="text-align:left;">
add home page information
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/brimittleman/threeprimeseq/4c26d4c1641e60f953fe953c04c7e6151ec4511e/docs/index.html" target="_blank">4c26d4c</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-05-01
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
Rmd
</td>
<td style="text-align:left;">
<a href="https://github.com/brimittleman/threeprimeseq/blob/539892a301ff49ee88909de2718bf6abac3f4155/analysis/index.Rmd" target="_blank">539892a</a>
</td>
<td style="text-align:left;">
Briana Mittleman
</td>
<td style="text-align:left;">
2018-05-01
</td>
<td style="text-align:left;">
Start workflowr project.
</td>
</tr>
</tbody>
</table>
</ul>
<p></details></p>
<hr />
<p>Briana Mittleman</p>
<p>This is the site I will use for my human 3’ seq project. I will have my workflow and analysis here. The three prime seq protocol I am using is Lexogen, QuantSeq 3’ mRNA-Seq library kit. The first analysis will be on the total and nucleic fractions of the LCL used in the net-seq analysis found at <a href="https://brimittleman.github.io/Net-seq/" class="uri">https://brimittleman.github.io/Net-seq/</a></p>
<div id="initial-analysis-on-rna-seq-of-nuclear-and-total-fractions" class="section level2">
<h2>Initial analysis on RNA seq of nuclear and total fractions:</h2>
<ul>
<li><a href="total.nuc.rnaseq.html">Initial data QC</a></li>
</ul>
<div id="initial-analysis-on-first-32-3-seq-libraries" class="section level3">
<h3>Initial analysis on first 32 3’ seq libraries:</h3>
<ul>
<li><a href="initial_map_qc.html">Initial mapping QC</a></li>
<li><a href="initial_gene_qc.html">Initial gene leve QC</a><br />
</li>
<li><a href="cov.analysis.threeprime1.html">Compare coverage in Three prime seq to RNAseq</a><br />
</li>
<li><a href="cov200bpwind.html">Coverage in 200bp bins</a><br />
</li>
<li><a href="dif.iso.usage.leafcutter.html">Differential isoform usage between fractions</a><br />
</li>
<li><a href="explore.filters.html">Explore filter cuttoffs</a><br />
</li>
<li><a href="enrichmentPAS.html">Enrichment at PAS</a><br />
</li>
<li><a href="comb.lanes.qc.html">Second Lane data</a></li>
</ul>
</div>
</div>
<div id="explore-and-filter-mis-primming" class="section level2">
<h2>Explore and filter mis-primming:</h2>
<ul>
<li><a href="a.content.html">Look at number of As in bins</a><br />
</li>
<li><a href="filter_As.html">Create script to filter mapped A’s</a><br />
</li>
<li><a href="cleanupdtseq.internalpriming.html">Test cleanUpdTSeq for calling internal priming</a><br />
</li>
<li><a href="peak.cov.pipeline.html">Pipeline to create peaks and clean them</a></li>
</ul>
</div>
<div id="peak-calling" class="section level2">
<h2>Peak calling:</h2>
<ul>
<li><a href="test.max2.html">Testing macs2 on 3’seq data</a><br />
</li>
<li><a href="deNovopeakcalling.html">Call peak regions de-novo</a></li>
<li><a href="eval.brain.html">Compare peaks in Derti Brain set</a><br />
</li>
<li><a href="test.smash.html">Test SMASH smoothing</a><br />
</li>
<li><a href="expand.smash.html">Expand SMASH analysis for use on midway</a><br />
</li>
<li><a href="dataprocfigures.html">Data Processing Figure design</a></li>
</ul>
<div id="peak-coveragenominal-qtlsdiff-iso" class="section level3">
<h3>Peak coverage/Nominal QTLs/Diff iso:</h3>
<ul>
<li><a href="28ind.peak.explore.html">Start evaluating peak quantificaiton</a><br />
</li>
<li><a href="pheno.leaf.comb.html">Prepare the data for leafcutter QTL calling</a></li>
<li><a href="apaQTLwLeafcutter.html">Call nominal QTLs</a><br />
</li>
<li><a href="diff_iso_pipeline.html">Differential Isoform pipeline</a></li>
</ul>
</div>
<div id="rerun-analysis-opp-strand" class="section level3">
<h3>Rerun analysis opp strand:</h3>
<ul>
<li><a href="peakOverlap_oppstrand.html">Rerun QTL analysis with off strand</a></li>
</ul>
</div>
<div id="evaluate-and-learn-from-qtls" class="section level3">
<h3>Evaluate and learn from QTLs:</h3>
<ul>
<li><a href="overlap_qtls.html">Overlap QTLs with other molecular QTLs</a></li>
</ul>
</div>
</div>
<div id="analysis-for-all-39-indivduals" class="section level2">
<h2>Analysis for all 39 indivduals:</h2>
<ul>
<li><p><a href="39indQC.html">Read and peak QC plots</a></p></li>
<li><p><a href="genometrack_figs.html">Genome tracks to visualize reads</a></p></li>
<li><p><a href="apaQTLsAllInd.html">APAqtl for full ind set</a></p></li>
<li><p><a href="PeakToGeneAssignment.html">QTL and Diff iso wih correct peak to gene assignment</a></p></li>
<li><p><a href="conditionAPAqtlFraction.html">Condition Total and Nuclear QTLs on each other</a></p></li>
<li><p><a href="characterizeTotalApaQtls.html">Characterize Total Apa QTLS</a></p></li>
<li><p><a href="characterizeNuclearApaQtls.html">Characterize Nuclear Apa QTLS</a></p></li>
<li><p><a href="chromHmm_enrichment.html">ChromHMM enrichment analysis</a></p></li>
<li><p><a href="apaQTLoverlapGWAS.html">Overlap with GWAS</a></p></li>
<li><p><a href="peakGeneCovEx.html">Visualize peaks in significant genes</a></p></li>
<li><p><a href="modifyLeafcutter.html">Look at filtering low peaks and modify leafcutter</a></p></li>
</ul>
<div id="molecular-qtl-analysis-and-overlap" class="section level3">
<h3>Molecular QTL analysis and Overlap:</h3>
<ul>
<li><p><a href="callMolQTLS.html">Rerun molecular QTLs</a></p></li>
<li><p><a href="overlapMolQTL.html">Make overlap QTL plots</a></p></li>
<li><p><a href="swarmPlots_QTLs.html">Plot top apaQTLs in other phenotypes</a></p></li>
<li><p><a href="locusZoom.html">LocusZoom plot for example QTLs</a></p></li>
<li><p><a href="overlapMolQTL.opposite.html">Overlap QTLs starting with APAqtls</a></p></li>
<li><p><a href="apa_prot_overlap.html">Investigate APA protein RNA relationship</a></p></li>
<li><p><a href="flash2mash.html">Use flash and mash to look at sharing</a></p></li>
<li><p><a href="explainpQTLs.html">Linear models to explain pQTLS</a></p></li>
</ul>
<p>Until now I have been focusing on way to develop the story for the paper. The next steps will be to systematically understand the data in order to filter to high quality data to use in the final analysis.</p>
<ul>
<li><p><a href="understandPeaks.html">Investigate Peak quality</a></p></li>
<li><p><a href="QTLsbyPCnum.html">Investigate Effect of included PCs on QTL number</a></p></li>
<li><p><a href="InvestigatePeak2GeneAssignment.html">Peak to gene assignment</a></p></li>
<li><p><a href="CompareLianoglouData.html">Look at our peaks compared to peaks from Lianogluo et al</a></p></li>
<li><p><a href="CovariateOnPCs.html">Explore cofactors agaisnt PCs for 39ind</a></p></li>
<li><p><a href="mispriming_approach.html">Deal with Mispriming problem</a></p></li>
<li><p><a href="NewPeakPostMP.html">Create new peaks after mispriming filter</a></p></li>
<li><p><a href="peakQCPPlots.html">QC plots peaks &gt;5% usage</a></p></li>
</ul>
</div>
</div>

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