Hi,
I want to use CuffDiff to call DE between two samples that I've aligned with TopHat.
Rather than creating a GTF via CuffLinks, I used one from UCSC (RefSeq). Since the manual suggests the GTF can be from sources other than CuffLinks, I assume this isn't a problem?
One thing that confuses me, however, is that CuffLinks seems to creating 0-based coordinates in its GTF (as per manual), while the GTF 2.2 standard calls for 1-based coordinates.
Since the UCSC GTF uses 1-based, does that mean UCSC GTF files are incompatible with CuffDiff?
Thanks,
Bio
I want to use CuffDiff to call DE between two samples that I've aligned with TopHat.
Rather than creating a GTF via CuffLinks, I used one from UCSC (RefSeq). Since the manual suggests the GTF can be from sources other than CuffLinks, I assume this isn't a problem?
One thing that confuses me, however, is that CuffLinks seems to creating 0-based coordinates in its GTF (as per manual), while the GTF 2.2 standard calls for 1-based coordinates.
Since the UCSC GTF uses 1-based, does that mean UCSC GTF files are incompatible with CuffDiff?
Thanks,
Bio
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