having problem with cufflinks output
Hi
I have run tophat with --GTF option and also run cufflinks with --GTF option too. The 7 cloumn of transcript.gtf file should be '+', '-' or '.', however I got 0 for all genes in 7 cloumn. I am wondering if anybody met the same problem before?
thank you
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Are you sure you're looking at the correct column (and not column 8)? Can you post a few lines of the file?
I have run tophat with
--GTFoption and also run cufflinks with--GTFoption too. The 7th column of transcript.gtf file should be '+', '-' or '.', however I got 0 for all genes in 7 cloumn. I am wondering if anybody met the same problem before?