Tophat strand-specific RNAseq- Do i need to reverse-complement?

[abhinay]

Hi all
I have strand-specific RNAseq data ( using Truseq kit- dUTP method) and I aligned the reads onto the genome with Tophat using --library-type=fr-firststrand option.
But when I visualized the output ( in Artemis), it was not strand-specific. But then with a weird guess, I reverse-complemented the fastq file of Read1 and voila- there was strand-specificity. Could anyone explain this to me. I could not find any mention of this tweak anywhere (including the latest nature methods paper). Is it something very natural to do that no one mentions it?? Im a novice in bioinformatics analysis, so not able to grasp this concept!
Thanks in advance!

[gokhulkrishnakilaru]

Dear Abhinay,

I used the same fr-firststrand with tophat but didn't see the strand specificity.

Could you please share more in detail about the reverse complimenting step that you did?

Thanks in advance.