Hi,
I am looking for a solution to the following situation :
If I use unstranded RNA-Seq data through Tophat, then Cufflinks, finally Cuffmerge, I have a new GTF file with a set of transcripts newly identified. As the input was unstranded, those new transcripts have no orientation in the merged GTF file (i.e. a point (".") on the 7th column instead of a plus ("+") or a minus ("-")).
However, the first step in the RSEM pipeline (labelled : "rsem-prepare-reference"), fails due to the point on the 7th column. It is waiting for either a plus or a minus, nothing else.
I use cufflinks/cuffmerge before RSEM, because RSEM does not detect new isoforms in RNA-Seq data.
Many thanks in advance for your advices,
Thibault
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Thibault D.
You can just replace the "." with a "+" or "-". With unstranded data it won't matter which you use, in fact. Something like awk 'BEGIN{FS="\t"}{if($7==".") {$7 = "+"} print $0}' foo.gtf > foo.fixed.gtf should work (I don't recall if you need OFS="\t").
Thank you for your answer, Devon
I thought it was not right to add it that way, and that it was the reason RSEM did not add a random strand by itself. I'll consider this option next time.
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