Tophat/Cufflinks for stranded RNA-seq data

Question

[marina.v.yurieva]

I have a naive question: what happens if I add "fr-firststrand" option when I run Tophat but don't add it for Cufflinks?

Answer 1

[Devon Ryan]

If your data is stranded, then you'll get slightly more accurate alignments and novel genes assembled by cufflinks won't have a meaningful strand assigned to them.

[marina.v.yurieva]

Ok, makes sense. Thank you!