Question: TEQC see all the reads with a given coverage
gravatar for nac
5.5 years ago by
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$ID), , drop=TRUE] #calculate the coverage Coverage <-, targets, perTarget=T, perBase=T) #from this coverage calculation I use the histogram function to plot the coverage coverage.hist(Coverage$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:"" pipermail="" bioconductor="" attachments="" 20120516="" be4f76e2="" attachment.pdf="">
ADD COMMENTlink written 5.5 years ago by nac280
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 154 users visited in the last hour