[BioC] Extract junction reads from bam

Helen Zhou zhou.helen at yahoo.com
Wed Aug 20 19:25:51 CEST 2014

Dear Wei and Michael,

thank you both for your helpful comments. This was just what I was looking for.

H Zhou

On Monday, 18 August 2014, 15:35, Wei Shi <shi at wehi.EDU.AU> wrote:

Dear Helen,

If you just want to get the number of reads mapping to that junction (not the actual reads), you can try featureCounts function in Rsubread package. It has a parameter called 'countSplitAlignmentsOnly' which allows you to count exon-spanning reads only. It is extremely fast.

Best wishes,

On Aug 19, 2014, at 6:32 AM, Helen Zhou wrote:

> Dear Sir/Madam,
> I have a bam file with reads from a paired-end RNA-seq experiments, and I would like to extract all reads that span a particular intron/exon junction. For example where part of a read maps to exon ABC starting at chr 1 position 66909348. I do not know where the first part of the read maps; there are multiple possible exons being spliced to exon ABC.
> I can extract all reads mapping to and spanning for example 50nt around the junction, saying:
> library(GenomicRanges)
> loc <-RangesList('1'=IRanges(start=6690298,end=6690398)) 
> parameter <- ScanBamParam(which=loc, what=extract, simpleCigar=FALSE, reverseComplement=FALSE)
> aln <- readGAlignmentsFromBam("test.bam", param=parameter)
> However, this includes all the reads that span across this region because the ends of the read map outside the area indicated in 'loc'. How can I get only the reads where (part of) the read starts mapping at the exact intron/exon location at position 66909348?
> Thanks you
> H Zhou
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