[BioC] TEQC see all the reads with a given coverage

[nathalie]

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




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