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Question: TEQC see all the reads with a given coverage
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gravatar for nac
5.5 years ago by
nac280
nac280 wrote:
HI all, I am using TEQC to have a look at coverage on my custom pull down sequencing #bam file reads<-get.reads("./13.bam",filetype="bam") #target file from which the baits has been designed: targets<-get.targets("target.txt", chrcol=1,startcol=2,endcol=3, zerobased=F, sep="\t",skip=0) readpairs<-reads2pairs(reads) #drop the pairs which are not matched: reads<-reads[!(reads$ID %in% readpairs$singleReads$ID), , drop=TRUE] #calculate the coverage Coverage <- coverage.target(reads, targets, perTarget=T, perBase=T) #from this coverage calculation I use the histogram function to plot the coverage coverage.hist(Coverage$coverageTarget, covthreshold=1000) I have quite a high coverage as I am pulling down a small region and use high seq lane to sequence . I have attached the coverage histograms, how do you pull out reads with a specific coverage from that coverage object? Another question, what does the fraction of target bases correspond to (left Y axis on histogram plots) Example: I want to see the position of all the reads with a coverage below 500? thanks Nat > sessionInfo() R version 2.15.0 (2012-03-30) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=C [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] TEQC_2.4.0 hwriter_1.3 Rsamtools_1.8.4 [4] Biostrings_2.24.1 GenomicRanges_1.8.3 IRanges_1.14.2 [7] BiocGenerics_0.2.0 loaded via a namespace (and not attached): [1] Biobase_2.16.0 bitops_1.0-4.1 stats4_2.15.0 zlibbioc_1.2.0 -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. -------------- next part -------------- A non-text attachment was scrubbed... Name: coverageHistograms_TEQC.pdf Type: application/pdf Size: 665466 bytes Desc: not available URL: <https: stat.ethz.ch="" pipermail="" bioconductor="" attachments="" 20120516="" be4f76e2="" attachment.pdf="">
ADD COMMENTlink written 5.5 years ago by nac280
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