Does the column "strand" represent the read strand of transcripts in cufflinks "transcripts.gtf" if my library is not strand-specific?

Question

[Alex Voronin]

If my library is not strand-specific, does the column "strand" mean the strand guessed by cufflinks or mean nothing in the file transcripts.gtf of cufflinks results?

Answer 1

[Juke34]

Cufflinks is inferring the strand looking at the splice site junctions. So, for unstranded library it should not guess the strand for single exon transcripts. You should in that case have a dot instead.

Actually this is a good question. I never checked the single exon case for the non-stranded librairy to be sure that they are not stranded by cufflinks.