Last updated: 2018-07-03

workflowr checks: (Click a bullet for more information)

• ✔ R Markdown file: up-to-date

  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.

• ✔ Repository version: 06ba744

  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.
  
  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 wflow_publish or wflow_git_commit). 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:

  
  Ignored files:
      Ignored:    .DS_Store
      Ignored:    .RData
      Ignored:    .Rhistory
      Ignored:    .Rproj.user/
      Ignored:    data/.DS_Store
  
  Untracked files:
      Untracked:  Ggsb_logo.r.pdf
      Untracked:  Rplot.pdf
      Untracked:  _workflowr.yml
      Untracked:  analysis/filter_bam.Rmd
      Untracked:  analysis/gencode.v19.annotation.proteincodinggene.saf
      Untracked:  analysis/temp
      Untracked:  analysis/top5_gen_wind200.bed
      Untracked:  data/DaPars_APA_geuvadis.txt
      Untracked:  data/Day7_cardiomyocytes_droNC_seq.bam
      Untracked:  data/Day7_cardiomyocytes_droNC_seq.bam.bai
      Untracked:  data/Day7_cardiomyocytes_drop_seq.bam
      Untracked:  data/Day7_cardiomyocytes_drop_seq.bam.bai
      Untracked:  data/LCL_3utr.txt
      Untracked:  data/LCL_3utrAB.bed
      Untracked:  data/LCL_3utrAB.neg.chr20.bed
      Untracked:  data/LCL_3utrAB_pos.chr1.bed
      Untracked:  data/LCL_3utrAB_pos.chr21.bed
      Untracked:  data/NET3-18486.gene.coverage.bed
      Untracked:  data/NET3-18486.gene.coverage.noSM.bed
      Untracked:  data/NET3-18486.gene.coverage.nosn.nosno.bed
      Untracked:  data/NET3-18486.gene.coverage.notopwind.bed
      Untracked:  data/NET3-18486.tss.coverage.bed
      Untracked:  data/NET3-18486_combined_Netpilot-sort.FC200.cov.bed
      Untracked:  data/NET3-18486_combined_Netpilot-sort.FC200.cov.no0.bed
      Untracked:  data/NET3-18486_combined_Netpilot-sort.exon.cov.txt
      Untracked:  data/NET3-18505.gene.coverage.bed
      Untracked:  data/NET3-18505_combined_Netpilot-sort.FC200.cov.no0.bed
      Untracked:  data/NET3-18508_combined_Netpilot-sort.FC200.cov.no0.bed
      Untracked:  data/NET3-19128_combined_Netpilot-sort.FC200.cov.no0.bed
      Untracked:  data/NET3-19141_combined_Netpilot-sort.FC200.cov.no0.bed
      Untracked:  data/NET3-19193_combined_Netpilot-sort.FC200.cov.no0.bed
      Untracked:  data/NET3-19239_combined_Netpilot-sort.FC200.cov.no0.bed
      Untracked:  data/NET3-19257_combined_Netpilot-sort.FC200.cov.no0.bed
      Untracked:  data/RNAseqGeuvadis_STAR_18486.coverage.bed
      Untracked:  data/RNAseqGeuvadis_STAR_18486.gene.coverage.bed
      Untracked:  data/RefSeqGenes.bed
      Untracked:  data/SRR1575922-sort.bam
      Untracked:  data/SRR1575922-sort.bam.bai
      Untracked:  data/SwitchGear_TSS.bed
      Untracked:  data/UMI_18486_dep_stat.txt
      Untracked:  data/UMI_18486_dep_stat_tab.txt
      Untracked:  data/UMI_18508_dep_stat.txt
      Untracked:  data/UMI_18508_nondep_stat.txt
      Untracked:  data/UMI_19238_dep_stat.txt
      Untracked:  data/UMI_Net3_18486_dedupstat.txt
      Untracked:  data/UMI_Net3_18486_stat.txt
      Untracked:  data/UMI_Net3_18505_dedupstat.txt
      Untracked:  data/UMI_Net3_18505_stat.txt
      Untracked:  data/UMI_Net3_18508_dedupstat.txt
      Untracked:  data/UMI_Net3_18508_stat.txt
      Untracked:  data/UMI_Net3_19128_dedupstat.txt
      Untracked:  data/UMI_Net3_19128_stat.txt
      Untracked:  data/UMI_Net3_19141_dedupstat.txt
      Untracked:  data/UMI_Net3_19141_stat.txt
      Untracked:  data/UMI_Net3_19193_dedupstat.txt
      Untracked:  data/UMI_Net3_19193_stat.txt
      Untracked:  data/UMI_Net3_19239_dedupstat.txt
      Untracked:  data/UMI_Net3_19239_stat.txt
      Untracked:  data/UMI_Net3_19257_dedupstat.txt
      Untracked:  data/UMI_Net3_19257_stat.txt
      Untracked:  data/UMI_mayer_stat.txt
      Untracked:  data/YG-SP-NET1-18486-dep-2017-10-13_S4_R1_001-sort.dedup.cov.bed
      Untracked:  data/YG-SP-NET3-18486_combined_Netpilot-sort.cov.AC093901.bed
      Untracked:  data/YG-SP-NET3-18486_combined_Netpilot-sort.cov.BTRC.bed
      Untracked:  data/YG-SP-NET3-18486_combined_Netpilot-sort.cov.RNU5B.bed
      Untracked:  data/YG-SP-NET3-18486_combined_Netpilot-sort.cov.WDR74.bed
      Untracked:  data/YG-SP-NET3-18486_combined_Netpilot-sort.cov.chr2.bed
      Untracked:  data/YG-SP-NET3-18486_combined_Netpilot-sort.cov.insig2.bed
      Untracked:  data/YG-SP-NET3-18486_combined_Netpilot-sort.cov.ppef2.bed
      Untracked:  data/YG-SP-NET3-18486_combined_Netpilot-sort.cov.rnu259p.bed
      Untracked:  data/YG-SP-NET3-18486_combined_Netpilot-sort.dedup.cov.insig2.bed
      Untracked:  data/all_RNAmetrics.picard.none.csv
      Untracked:  data/all_files.APA500.coverage.bed
      Untracked:  data/all_files_coverage.bed
      Untracked:  data/all_strand_genecounts_18486.txt
      Untracked:  data/bam_files_chr/
      Untracked:  data/blcl.hg38.sorted.bam
      Untracked:  data/blcl.hg38.sorted.bam.bai
      Untracked:  data/cell_growth_3.21.18.csv
      Untracked:  data/clip_18486_dep.txt
      Untracked:  data/clusters.bed
      Untracked:  data/clusters.hg38
      Untracked:  data/clusters.hg38.3utr.neg.bed
      Untracked:  data/clusters.hg38.3utr.pos.bed
      Untracked:  data/clusters.hg38.bed
      Untracked:  data/dedup_18486_mapqual.txt
      Untracked:  data/drop7_cardio_3utr.txt
      Untracked:  data/drop7_cardio_3utrAB.neg.chr21.bed
      Untracked:  data/drop7_cardio_3utrAB.pos.chr21.bed
      Untracked:  data/ensembl2refseq.txt
      Untracked:  data/eqtl_fullgene/
      Untracked:  data/eqtl_genes_effectsize.txt
      Untracked:  data/eqtl_output.cis.txt
      Untracked:  data/eqtl_output.txt
      Untracked:  data/eqtl_strand_spec/
      Untracked:  data/exon_cov/
      Untracked:  data/fc_genecov/
      Untracked:  data/gencode.v19.annotation.distfilteredgenes.bed
      Untracked:  data/gencode.v19.annotation.egqtlfilter.bed
      Untracked:  data/gencode.v19.annotation.eqtlfilter.bed
      Untracked:  data/gencov_18486.bed
      Untracked:  data/gene_cov_count/
      Untracked:  data/gene_coverage_18486_dedup_hist.txt
      Untracked:  data/gene_coverage_18486_hist.txt
      Untracked:  data/gene_coverage_18508_dep.txt
      Untracked:  data/gene_coverage_18508_dep_hist.txt
      Untracked:  data/gene_coverage_18508_nondep_hist.txt
      Untracked:  data/gene_coverage_19238_dep_hist.txt
      Untracked:  data/gene_coverage_mayer_SRR1575922_hist.txt
      Untracked:  data/gene_dedup_cov_count/
      Untracked:  data/genotypes.rs7144811.txt
      Untracked:  data/growth_curve_3.16.csv
      Untracked:  data/hES.hg38.sorted.bam
      Untracked:  data/hES.hg38.sorted.bam.bai
      Untracked:  data/hg19.GM72.CTCF
      Untracked:  data/hg19.ref.genes.bed
      Untracked:  data/insig2sec.txt
      Untracked:  data/mapped_18486_dep.txt
      Untracked:  data/mapped_18486_dep_max.txt
      Untracked:  data/mapped_18508_dep.txt
      Untracked:  data/mapped_19238_dep.txt
      Untracked:  data/mapped_mayer.txt
      Untracked:  data/mapped_qual_18486.txt
      Untracked:  data/mapped_qual_18505.txt
      Untracked:  data/mapped_qual_18508.txt
      Untracked:  data/mapped_qual_19128.txt
      Untracked:  data/mapped_qual_19141.txt
      Untracked:  data/mapped_qual_19193.txt
      Untracked:  data/mapped_qual_19239.txt
      Untracked:  data/mapped_qual_19257.txt
      Untracked:  data/matrix_expression.txt
      Untracked:  data/matrix_genotypes.csv
      Untracked:  data/matrix_genotypes.txt
      Untracked:  data/merged_Net1.bam
      Untracked:  data/merged_Net1.bam.bai
      Untracked:  data/meta_info_coverage.bed
      Untracked:  data/names_geno.txt
      Untracked:  data/net-3-readmap/
      Untracked:  data/net1_18486_dep_dedup.bed
      Untracked:  data/net1_18486_dep_dedup_chr.bed
      Untracked:  data/net4_readcounts.xlsx
      Untracked:  data/net_pilot_eqtl_expression.bed
      Untracked:  data/net_pilot_eqtl_genotypes.vcf
      Untracked:  data/netcomb_intronicbases.csv
      Untracked:  data/opp_strand_genecounts_18486.txt
      Untracked:  data/opp_strand_genecounts_18505.txt
      Untracked:  data/opp_strand_genecounts_filt_18486.txt
      Untracked:  data/perc_alive_3.16.csv
      Untracked:  data/prom_coverage/
      Untracked:  data/qual_18486_dep.txt
      Untracked:  data/qual_18508_dep.txt
      Untracked:  data/qual_19238_dep.txt
      Untracked:  data/qual_mayer.txt
      Untracked:  data/refseq_250up.bed
      Untracked:  data/run_lm_APA.txt
      Untracked:  data/same_strand_genecounts_18486.txt
      Untracked:  data/same_strand_genecounts_18505.txt
      Untracked:  data/same_strand_genecounts_filt_18486.txt
      Untracked:  data/sort_dedup_3prime_chr2_no0.18486.txt
      Untracked:  data/sort_dedup_chr2_no0_18486.txt
      Untracked:  data/test.txt
      Untracked:  data/three_prime_utr.bed
      Untracked:  data/top5_exonlist.txt
      Untracked:  data/top5_exonlist_18486_fiveprime_cov.txt
      Untracked:  data/top5_exonlist_18486_fiveprime_cov2.txt
      Untracked:  data/top5_exonlist_18486_fiveprime_cov2_filter.txt
      Untracked:  data/top5_exonlist_18486_threeprime_cov.txt
      Untracked:  data/top5_exonlist_18486_threeprime_cov2.txt
      Untracked:  data/top5_exonlist_18486_threeprime_cov2_filter.txt
      Untracked:  data/top5_gen_wind200.bed
      Untracked:  data/top5_gen_wind200.tab.bed
      Untracked:  data/uniq_genes/
      Untracked:  data/windows_200/
      Untracked:  docs/temp
      Untracked:  docs/top5_gen_wind200.bed
      Untracked:  output/Rs7144811_apa_usage.pdf
      Untracked:  output/picard.accrossgenebodies.netpilot.csv
  
  Unstaged changes:
      Modified:   analysis/APA_qtl_RNAseq.Rmd
      Modified:   analysis/LCL_growth.Rmd
      Modified:   analysis/Net_3_explore.Rmd
      Modified:   analysis/Reads_per_pas.Rmd
      Modified:   analysis/UTR_coverage.Rmd
      Modified:   analysis/_site.yml
      Modified:   analysis/about.Rmd
      Modified:   analysis/bin_windows.Rmd
      Modified:   analysis/check_bamid.Rmd
      Deleted:    analysis/chunks.R
      Modified:   analysis/conda.environment.Rmd
      Modified:   analysis/config.snake.setup.Rmd
      Modified:   analysis/create_blacklist.Rmd
      Modified:   analysis/data_for_ggplot.Rmd
      Modified:   analysis/eqtl_bystrand.Rmd
      Modified:   analysis/explore_umi_usage.Rmd
      Modified:   analysis/extend_APA_qtl.Rmd
      Modified:   analysis/gviz_plots.Rmd
      Modified:   analysis/initial.data.exploration.Rmd
      Modified:   analysis/license.Rmd
      Modified:   analysis/map_stats_from_bam.Rmd
      Modified:   analysis/reads_in_genes.Rmd
      Modified:   analysis/recreate_mayer_figs.Rmd
      Modified:   analysis/strand_spec.Rmd
      Modified:   analysis/test-analysis.Rmd
      Modified:   analysis/three_prime_UTR.Rmd
      Modified:   analysis/update_snakefile.Rmd
      Modified:   analysis/use_deeptools.Rmd
      Modified:   analysis/visualize_genomefeatures.Rmd
  
  

  Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.

Expand here to see past versions:

File	Version	Author	Date	Message
html	363ea13	Briana Mittleman	2018-06-22	Build site.
Rmd	97a0c53	Briana Mittleman	2018-06-22	wflow_publish(c(“analysis/index.Rmd”, “analysis/net-4-explore.Rmd”))
html	d76f54d	Briana Mittleman	2018-04-05	Build site.
Rmd	c269f0f	Briana Mittleman	2018-04-05	fixr eqtl by strand bullet
html	465e616	Briana Mittleman	2018-04-03	Build site.
html	0a0b388	Briana Mittleman	2018-03-22	Build site.
Rmd	0e50352	Briana Mittleman	2018-03-22	start strand specific analysis
html	09e78cf	Briana Mittleman	2018-03-19	Build site.
Rmd	3aa98a8	Briana Mittleman	2018-03-19	add recreate rmd to index
html	fd42b70	Briana Mittleman	2018-03-16	Build site.
Rmd	1707538	Briana Mittleman	2018-03-16	initialize growth analysis
html	b789dd9	Briana Mittleman	2018-03-02	Build site.
Rmd	646ee57	Briana Mittleman	2018-03-02	initialize analysis for the pilot data
html	a84f24a	Briana Mittleman	2018-02-14	Build site.
html	d72c447	Briana Mittleman	2018-02-02	Build site.
Rmd	01f846f	Briana Mittleman	2018-02-02	wflow_publish(c(“index.Rmd”, “use_deeptools.Rmd”))
html	558ff5a	Briana Mittleman	2018-01-31	Build site.
Rmd	308d2b5	Briana Mittleman	2018-01-31	add utr cov to index
html	2f36a96	Briana Mittleman	2018-01-25	Build site.
Rmd	52df489	Briana Mittleman	2018-01-25	stranded graphs and add to index
html	8a554c1	Briana Mittleman	2017-12-13	Build site.
Rmd	3ed7074	Briana Mittleman	2017-12-13	create plots for actb and add to index
html	3326147	Briana Mittleman	2017-12-08	Build site.
Rmd	fab79ca	Briana Mittleman	2017-12-08	reforat gene count data for ggplot
html	f006037	Briana Mittleman	2017-11-30	Build site.
Rmd	b180d9a	Briana Mittleman	2017-11-30	fix index formating
html	ec2d994	Briana Mittleman	2017-11-30	Build site.
Rmd	35b1aa1	Briana Mittleman	2017-11-30	wflow_publish(c(“bin_windows.Rmd”, “index.Rmd”, “reads_in_genes.Rmd”))
html	552910d	Briana Mittleman	2017-11-28	Build site.
Rmd	7041a54	Briana Mittleman	2017-11-28	add reads_in_gene
html	697f6a0	Briana Mittleman	2017-11-20	Build site.
Rmd	560df7d	Briana Mittleman	2017-11-20	initiate the reads in gene analysis and add it to index
html	121c3e0	Briana Mittleman	2017-11-16	Build site.
Rmd	acd27cd	Briana Mittleman	2017-11-16	add map_stats to inde
html	3d6ebfe	Briana Mittleman	2017-11-09	Build site.
Rmd	aee8225	Briana Mittleman	2017-11-09	initialize and load data for genomation data
html	1d36dec	Briana Mittleman	2017-11-08	Build site.
Rmd	9a86ba3	Briana Mittleman	2017-11-08	Initiate the explore UMI usage analysis
html	4207b60	Briana Mittleman	2017-11-06	Build site.
Rmd	7eeb4e1	Briana Mittleman	2017-11-06	start initial data exploration and add it to index
Rmd	baeec88	Briana Mittleman	2017-10-26	commit index and config changes
html	5096c14	Briana Mittleman	2017-10-26	Build site.
Rmd	4c45592	Briana Mittleman	2017-10-26	add new config/snake file to index
html	0ea88cc	Briana Mittleman	2017-10-24	Build site.
Rmd	13f7b6a	Briana Mittleman	2017-10-24	move conda code to conda environment analysis and update
html	5f7df97	Briana Mittleman	2017-10-24	Build site.
Rmd	f03ffb4	Briana Mittleman	2017-10-17	add test analysis
html	e445d99	Briana Mittleman	2017-10-17	Build site.
html	6ee857d	Briana Mittleman	2017-10-17	Build site.
Rmd	c88cd2e	Briana Mittleman	2017-10-17	Publish the initial files for myproject
Rmd	d639248	Briana Mittleman	2017-10-17	Start workflowr project.

---

This is the workflowr site for my Net-seq project. I will have all of the data, code, and analysis here.

Set-up for mappping my libraries:

• Setting up conda environment

• Setting up config and snake files

Initial data exploration:

• Initial data exploration for NetSeq1 libary

• Explore read lengths that are mapping

• Explore the UMI usage in the NetSeq1 library

• Use the genomation package to vizualize genome features and see overlap with Net-seq1

• Exploration of read counts per gene

• Reformat gene counts for ggplot2 data analysis

• Explore read counts per genome bin

• Create IGV browser style plots

Initial analysis for Net-3:

• Net-3 Initial exploration

Net-pilot analysis:

• Update snakefile for pilot analysis

• Create blacklist to filter reads

• Recreate figures from Mayer

• Strand specific analysis

• Connect eQTLs to strand

Cell Growth analysis:

• Initial plots on growth

Exploration of the 3` seq and ApA sites:

• Look for read enrichment at ApA sites

• UTR coverage analysis

• Look at enrichment using Deep tools

Net 4 analysis- includes 3 lanes for all 16 individuals:

• Explore Net 4

---

---

---

This reproducible R Markdown analysis was created with workflowr 1.0.1

---