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Old 01-20-2015, 07:39 AM   #1
Location: paris

Join Date: Jan 2013
Posts: 10
Default generating pileup of paired end fragments

Dear all,
i'm working with paired end rnaseq data. i wanted to generate a pileup with samtools mpileup but noticed that only the mapping reads get counted, and not the unmapped part between two mates, like so:

______READ1--------READ2________ <- mapping
______1 1 1 1 0 0 0 1 1 1 1________ <- pileup

is generating pileups using the whole fragment (read + mate + part in between them) frowned upon for some reason? would it be correct to do it? if yes are there any tools?

alternatively, is there a tool to merge mates and generate the complete fragment in a sam file?

Thank you!

Last edited by Slacanch; 01-20-2015 at 07:42 AM.
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