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Thread | Thread Starter | Forum | Replies | Last Post |
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#1 | |||
Member
Location: Stockholm, Sweden Join Date: Oct 2009
Posts: 62
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Hi,
I have discovered some inconsistencies when browsing through the Cufflinks files transcripts.expr, transcripts.tmap and genes.expr. Multiple transcripts belonging to the same gene are not named accordingly in the different files. Here are two examples to illustrate: in transcripts.expr we have the two transcripts: Quote:
In the transcripts.gtf file however both "genes" are present: Quote:
A somewhat more complicated example is a loci with three different transcripts deemed to be present, see attached picture "loci30602.30603.30604.gif". Analougusly, the three transcripts have different gene names: Quote:
The FPKM value in the genes.expr file seems to be the total of all isoforms, but the naming and referencing is confusing. Now you know. Boel Last edited by Boel; 04-14-2010 at 06:06 AM. |
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#2 |
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Location: Carlsbad,CA Join Date: Jan 2010
Posts: 94
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Your figures are really hard to see! Can you put up a better quality image?
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#3 |
Member
Location: Stockholm, Sweden Join Date: Oct 2009
Posts: 62
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Yup, they got tiny when I attached them apperently. They can be viewed here:
http://picasaweb.google.se/108683670...Illustrations# |
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