hi,
I would like to estimate difference in expression using cuffdiff. The program requires a GTF file.
If I provide a standard annotation file (such as from UCSC), could I just skip running cufflinks?
On the other hand, if I do want to provide a GTF from cufflinks, which GTF do I provide? There are two samples to compare, and cufflinks must be run separately for each of those, resulting in two GTF trascript files.
Any suggestion?
I would like to estimate difference in expression using cuffdiff. The program requires a GTF file.
If I provide a standard annotation file (such as from UCSC), could I just skip running cufflinks?
On the other hand, if I do want to provide a GTF from cufflinks, which GTF do I provide? There are two samples to compare, and cufflinks must be run separately for each of those, resulting in two GTF trascript files.
Any suggestion?
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