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Old 11-14-2011, 06:38 PM   #1
camelbbs
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Default cuffmerge output

hi,

I run cuffmerge -g hg19_ucsc.gtf gtflist

and got the merged.gtf in the output folder.

1. Does this merged.gtf file include the reference gtf?

2. There is an output file called transcritp.gtf, anyone can tell me what its difference to merged.gtf

Thanks a lot!
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Old 11-15-2011, 11:46 AM   #2
cw11
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Regarding your first question: In Cufflinks, the -g option gives you reference annotation based assembly (described here), which means .gtf output should include the reference gtf plus any newly discovered transfrags. For Cuffmerge, the manual says that using the -g option means that the input assemblies are merged together with the reference GTF and included in the final output. So I believe your merged.gtf file should include the reference (plus any novel transfrags).

As for your second question, I was actually wondering this myself. I know that the merged.gtf file is what you have to input if you want to run CuffDiff (because it has the p_id and the tss_id and transcripts.gtf doesn't). But I'm not actually sure what the difference between them is. They're not the same size...

wc -l transcripts.gtf
421950 transcripts.gtf
wc -l merged.gtf
383010 merged.gtf

Does anybody else have thoughts?
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Old 11-17-2011, 09:06 AM   #3
camelbbs
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Quote:
Originally Posted by cw11 View Post
Regarding your first question: In Cufflinks, the -g option gives you reference annotation based assembly (described here), which means .gtf output should include the reference gtf plus any newly discovered transfrags. For Cuffmerge, the manual says that using the -g option means that the input assemblies are merged together with the reference GTF and included in the final output. So I believe your merged.gtf file should include the reference (plus any novel transfrags).

As for your second question, I was actually wondering this myself. I know that the merged.gtf file is what you have to input if you want to run CuffDiff (because it has the p_id and the tss_id and transcripts.gtf doesn't). But I'm not actually sure what the difference between them is. They're not the same size...

wc -l transcripts.gtf
421950 transcripts.gtf
wc -l merged.gtf
383010 merged.gtf

Does anybody else have thoughts?
There is no explanation for this file in cuffdiff documents. I hope someone can add it.
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Old 02-19-2013, 03:44 PM   #4
dvanic
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Has anyone found the answer to this?
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