Extract reads based on pair orientation

Hi!

I have paired-end mapped reads (using bbmap) that I would like to separate based on the orientation of the read pairs. I see pairs as being able to have the following orientations:

LR: --> <--

LL or RR: --> --> or <-- <--

RL: <-- -->

I've managed to separate the reads in two, namely LR and one with the others ("discordant") using samtools:

samtools view -b infile.bam -F 1294 > outfile.bam

Which I picked up here , but am not too sure about... In IGV I can colour these discordant reads according to 'pair orientation'. I can see that they group together according to read orientation in clearly defined genomic positions.

But I have no idea how to split them based on orientation from here...

I tried several options, including a tool in the Jvarkit (unable to complete make of BioAlcidae so could not run) and other custom scripts that did not work due being dependent on older versions of samtools/htslib...

I hope someone can help me from here - thanks! ^@^

sam bam read pair orientation paired end

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written 7.5 years ago by Emilie •

(unable to complete make of BioAlcidae so could not run

I need more information, or submit an issue: https://github.com/lindenb/jvarkit/issues

• 1 views • link

written 7.5 years ago by Pierre Lindenbaum

0 answers

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