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Old 02-11-2015, 12:02 PM   #28
Location: Mc Gill -- Montreal

Join Date: Dec 2013
Posts: 37

A possible problem :

According to htseq documentation :

"The fact that the records describe the same fragment can be seen from the fact that they have the same read name"

So Tophat for instance is ouputing read paris with different names. (Adding 1 or 2 at the end of the name)

So simply do that:

(samtools view -H in.bam; in.bam | awk '{print substr($1,1,length($1)-1),$0}' | sed 's/ [^ ]*//') | samtools view -bSh - > in.samereadname.bam
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