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Old 02-27-2014, 01:02 AM   #8
Location: Australia, Brisbane

Join Date: Nov 2012
Posts: 13

yes my gtf file contains all exon lines for antisense transcripts as well.
this explains the discrepancy since I used -s yes for the stranded libraries.
But why sometimes the counts are zero when the read maps to a position which is covered by a regular gene on one strand and a overlapping antisense gene on the opposite strand?

selecting -stranded yes should account for this,shouldn't it?

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