Last updated: 2019-02-26

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Knit directory: threeprimeseq/analysis/

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    Modified:   analysis/28ind.peak.explore.Rmd
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    Modified:   code/Snakefile

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File Version Author Date Message
Rmd 6637b21 Briana Mittleman 2019-02-26 add avg total usage
html b27ba86 Briana Mittleman 2019-02-26 Build site.
Rmd c5dfa4b Briana Mittleman 2019-02-26 fix file for ankeeta

Ankeeta has been working with 3 pac bio libraries for whole LCLs. The meged bam file has 4,164,259 reads. I want to look at how many of these reads cover my peaks. It would be best to know how many reads ends

I need to fix the strand for my peaks and give them to her.

fixPeaks4Ankeeta.py

In=open("/project2/gilad/briana/threeprimeseq/data/mergedPeaks_noMP_GeneLoc/Filtered_APApeaks_merged_allchrom_noMP.sort.named.noCHR_geneLocParsed_withAnno.SAF","r")
Out="/project2/yangili1/PAPeaks_STARMap_GeneLocAnno.bed"

def fix_strand(Fin,Fout):
    fout=open(Fout,"w")
    for n, ln in enumerate(Fin):
        if n == 0: 
            continue
        else: 
            id, chrom, start, end, strand = ln.split()
            if strand=="+":
                chromF="chr" + chrom
                peak=id.split(":")[0]
                geneLoc=id.split(":")[5:]
                geneLocF=":".join(geneLoc)
                newID=peak + ":" + geneLocF
                score="."
                fout.write("%s\t%s\t%s\t%s\t%s\t-\n"%(chromF,start,end,newID,score))
            else:
                chromF="chr" + chrom
                peak=id.split(":")[0]
                geneLoc=id.split(":")[5:]
                geneLocF=":".join(geneLoc)
                newID=peak + ":" + geneLocF
                score="."
                fout.write("%s\t%s\t%s\t%s\t%s\t+\n"%(chromF,start,end,newID,score))
    fout.close()
    
    
fix_strand(In, Out)

Add average usage to this:

use similar code to filter_5percUsagePeaks.R

counts only numeric are in /project2/gilad/briana/threeprimeseq/data/phenotypes_filtPeakTranscript_noMP_GeneLocAnno/filtered_APApeaks_merged_allchrom_refseqGenes.GeneLocAnno_NoMP_sm_quant.Total.fixed.pheno.CountsOnlyNumeric.txt I will take the mean for each row of this and use it as the score in the bed file.

Run this interactively

library(dplyr)
totUsage=read.table("/project2/gilad/briana/threeprimeseq/data/phenotypes_filtPeakTranscript_noMP_GeneLocAnno/filtered_APApeaks_merged_allchrom_refseqGenes.GeneLocAnno_NoMP_sm_quant.Total.fixed.pheno.CountsOnlyNumeric.txt", header=F)
peakBed=read.table("/project2/yangili1/PAPeaks_STARMap_GeneLocAnno.bed", header=F, col.names = c("chr", "start", "end", "ID", "score", "strand"), stringsAsFactors = F)


MeanUsage=rowMeans(totUsage)

outBed=as.data.frame(cbind(peakBed, MeanUsage)) %>% select(chr, start, end, ID, MeanUsage, strand)

write.table(outBed,file="/project2/yangili1/PAPeaks_STARMap_GeneLocAnno_withMeanUsage.bed", row.names=F, col.names=F, quote = F, sep="\t")  


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):
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 [5] backports_1.1.2 git2r_0.24.0    magrittr_1.5    evaluate_0.13  
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[13] tools_3.5.1     stringr_1.4.0   glue_1.3.0      yaml_2.2.0     
[17] compiler_3.5.1  htmltools_0.3.6 knitr_1.20