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Old 01-24-2016, 08:07 PM   #2
Location: Auckland

Join Date: Sep 2011
Posts: 72

XLOC numbers are assigned to all genes, not just ones that aren't in GTF files you supply. So some genes will end up with a gene_name, but all genes end up with a gene_id (=XLOC number). I think the issue is that the downstream programs are looking for the gene_id field and not the gene_name field.

Incidentally, as I am interpreting it, using the -G switch (as opposed to the -g switch) means that you'll only ever detect/quantitate/analyse genes that are in your GTF file (while using -g means that cufflinks will create a new gene from scratch if there is sufficient read support, even if it's not in the GTF file you supply).

So, with the code you used, all output genes should have both a gene_id (XLOC number) and a gene_name (from the GTF)
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