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Old 06-07-2010, 11:24 AM   #1
Location: Europe

Join Date: Apr 2010
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Default CuffLinks / CuffDiff GTF Compatibility


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?


Last edited by Bio.X2Y; 06-07-2010 at 11:26 AM. Reason: Got my 0s and 1s mixed up...
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Old 06-16-2010, 07:24 AM   #2
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I've raised this question on the Bowtie sourceforge (I can't find a place to raise CuffLinks specific questions/bugs):

Am I correct in thinking that the CuffLinks GTF files are non-standard? They use 0-based coordinates as per the manual, while GTF2.2 requires 1-based. Does this mean that CuffDiff is not compatible with UCSC or Ensembl GTFs?
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Old 08-17-2011, 08:04 AM   #3
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While describing the start column of the transcripts.gtf file, cufflinks manual ( states:

The leftmost coordinate of this record (where 1 is the leftmost possible coordinate)
Therefore, it should be 1-based.

Last edited by Marcelo_Alejandro; 08-17-2011 at 11:55 AM.
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