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Old 05-22-2014, 11:37 AM   #1
vramnarine
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Default Cufflinks, Cuffquant and Cuffdiff Parameters : multi-read and frag-bias correction

Hi All,

I am using the new Cufflinks workflow of:

Cufflinks -> Cuffmerge -> Cuffquant -> Cuffdiff

Within cufflinks I use the following parameters:
--frag-bias-correct
--multi-read-correct

Are these parameters necessary to set within cuffquant AND cuffdiff IF I have already done this correction within cufflinks.

IF so, it seems a bit redundant.

ANy clarity is much appreciated!
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Old 08-05-2014, 04:23 PM   #2
catbus
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Pretty sure you need to do it in BOTH cases. Note that CUFFDIFF does not actually directly make use of your Cufflinks results, except for the "merged.gtf."

It is in fact entirely possible to run CUFFDIFF without running Cufflinks at all.

Cuffdiff primarily operates on the input BAM files; it doesn't really care about (or use) the Cufflinks data except for the merged GTF file.
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Old 08-05-2014, 04:24 PM   #3
catbus
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To clarify, it's not that you need to do it in both cases per se, so much as the Cufflinks and Cuffdiff results are entirely independent EXCEPT for the "merged.gtf" file.

You will notice that the output of Cufflinks does NOT go into Cuffdiff at all except for the merged.gtf file. And in fact you can run Cuffdiff without ever using Cufflinks.
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