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Old 04-24-2012, 03:50 AM   #1
mattia
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Location: Milano

Join Date: Aug 2011
Posts: 30
Default cufflinks configuration

Hi,
I'm trying to define the best options configuration of Cufflinks. In order to estimate only known transcripts, is my command-line right or do I have to modify something?

cufflinks -u --compatible-hits-norm -b /human_hg19.fa -p 3 --library-type fr-secondstrand -G /transcripts.gtf -o output_dir /accepted_hits.bam

in which:
transcripts.gtf is the annotation file containing only known transcripts.

My data are generated from SOLiD 5500.

Thanks a lot,
Mattia
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Old 04-24-2012, 05:51 PM   #2
sdriscoll
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Posts: 438
Default

that should work.
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configuration, cufflink, known transcripts, normalization

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