Pipeline for 55 Ind

Last updated: 2019-02-01

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    Modified:   analysis/understandPeaks.Rmd
    Modified:   code/Snakefile

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File	Version	Author	Date	Message
Rmd	957a0ee	Briana Mittleman	2019-02-01	initiate 55 ind pipeline

First I need to move the duplicate files to a different dir. data/Replicates

YL-SP-18499-N-batch4.combined-sort.bed YL-SP-18499-T-batch4.combined-sort.bed

YL-SP-18912-N-batch4.combined-sort.bed YL-SP-18912-T-batch4.combined-sort.bed

YL-SP-19093-N-batch4.combined-sort.bed YL-SP-19093-T-batch4.combined-sort.bed

YL-SP-19140-N-batch4.combined-sort.bed YL-SP-19140-T-batch4.combined-sort.bed

-Bedsort
-sort

Remove 18497-N (18499) 18497-T (18499) 18500-N (18501) 18500-T (18501)

Mispriming
- Get 10 basepairs upstream: wrap_Upstream10Bases.sh
- Find sequence for these regions: Nuc10BasesUp.sh
- find which are bad run_filterMissprimingInNuc10.sh - filter bed file run_filterSortBedbyCleanedBed.sh - sort clean bed file sort_filterSortBedbyCleanedBed.sh - filter bam files wrap_filterBamforMP.pysam2.sh
- sort and index clean bam SortIndexBam_noMP.sh - merge clean bam files mergeBamFiles_noMP.sh
- sort and index merged SortIndexMergedBam_noMP.sh
- create BW mergedBam2Bedgraph.sh
- make it a coverage file run_bgtocov_noMP.sh - call peaks run_callPeaksYL_noMP.sh
- filter peaks - cat /project2/gilad/briana/threeprimeseq/data/mergedPeaks_noMP/*.bed > /project2/gilad/briana/threeprimeseq/data/mergedPeaks_noMP/APApeaks_merged_allchrom_noMP.bed - make SAF file bed2saf_noMP.py - run feature counts peak_fc_noMP.sh - filter peaks run_filter_peaks_noMP.sh
- name peaks

x = wc -l /project2/gilad/briana/threeprimeseq/data/mergedPeaks_noMP_filtered/Filtered_APApeaks_merged_allchrom_noMP.bed

seq 1 x > peak.num.txt

sort -k1,1 -k2,2n Filtered_APApeaks_merged_allchrom_noMP.bed > Filtered_APApeaks_merged_allchrom_noMP.sort.bed

paste /project2/gilad/briana/threeprimeseq/data/mergedPeaks_noMP_filtered/Filtered_APApeaks_merged_allchrom_noMP.sort.bed peak.num.txt | column -s $'\t' -t > temp
awk '{print $1 "\t" $2 "\t" $3 "\t" $7  "\t"  $4 "\t"  $5 "\t" $6}' temp >   /project2/gilad/briana/threeprimeseq/data/mergedPeaks_noMP_filtered/Filtered_APApeaks_merged_allchrom_noMP.sort.named.bed

#cut the chr  

sed 's/^chr//' /project2/gilad/briana/threeprimeseq/data/mergedPeaks_noMP_filtered/Filtered_APApeaks_merged_allchrom_noMP.sort.named.bed > /project2/gilad/briana/threeprimeseq/data/mergedPeaks_noMP_filtered/Filtered_APApeaks_merged_allchrom_noMP.sort.named.noCHR.bed

Gene assignments mapnoMPPeaks2GenomeLoc.sh
make SAF processGenLocPeakAnno2SAF.py
feature counts GeneLocAnno_fc_TN_noMP.sh
fix header fix_head_fc_geneLoc_tot_noMP.py
fix header fix_head_fc_geneLoc_nuc_noMP.py
make phenotype run_makePhen_sep_GeneLocAnno_noMP.sh
convert to usage pheno2CountOnly_genelocAnno.R
counts to numeric convertCount2Numeric_noMP_GeneLocAnno.py

Make script to filter 5%

Session information

sessionInfo()

R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS  10.14.1

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
 [1] workflowr_1.1.1   Rcpp_0.12.19      digest_0.6.17    
 [4] rprojroot_1.3-2   R.methodsS3_1.7.1 backports_1.1.2  
 [7] git2r_0.23.0      magrittr_1.5      evaluate_0.11    
[10] stringi_1.2.4     whisker_0.3-2     R.oo_1.22.0      
[13] R.utils_2.7.0     rmarkdown_1.10    tools_3.5.1      
[16] stringr_1.3.1     yaml_2.2.0        compiler_3.5.1   
[19] htmltools_0.3.6   knitr_1.20

This reproducible R Markdown analysis was created with workflowr 1.1.1

Pipeline for 55 Ind

Briana Mittleman

2/1/2019

Session information