TopHat for directionnal RNA seq

[ClemBuntu]

Hello,

I've mapped some reads with tophat using "fr-firststrand" option. I'm on single read, I excepected all my reads will be in the same strand but viewing my .bam file with IGV it looks like I got reads both orientation on my reads : http://imgur.com/GKCLibr (ie arrow are not in the same direction)

How is that possible ? Does that make sence ?

[mastal]

It depends what platform and what library type was used to generate the reads.

[ClemBuntu]

Library were made with Rapid Illumina RNA-Seq Library Prep Kit and it was sequenced with illumina.

[mastal]

Unless a stranded library prep is used you expect to see reads mapping to both strands, so you can't tell which strand the transcript comes from.