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Old 07-28-2011, 06:40 AM   #1
ega2d
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Location: Virginia

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Default GTF/GFF3 format and new Cufflinks

Hi all,

I have sucessfully completed an RNAseq pipeline with the old version of Cufflinks and I'm now trying to run the same data through the new versions of Tophat and Cufflinks. Namely, I'm hoping to add on all the bells and whistles of the new Cufflinks (bias correction, multi-read correct, and RABT).

My problem seems to be in implementing the RABT portion of Cufflinks. I suspect it might be a problem with the format of my GFF3 annotation. Could anyone who has successfully run the new version of Cufflinks please post a few lines of their annotation file?

Also, for researchers working on "more" complete genomes, how did you handle the completed-ness of the genome annotation vs. the increase in false-positives as was mentioned in the Roberts et al paper describing RABT?

Any help would be GREATLY appreciated!!!
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Old 07-28-2011, 10:44 AM   #2
DZhang
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Hi,

Check this link (http://cufflinks.cbcb.umd.edu/gff.html) if you have not. The tool gffread can help you verify if your GFF3 annotation is in the right format.

Hope this helps.

Douglas
www.contigexpress.com
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Old 08-02-2011, 01:40 PM   #3
pbluescript
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Illumina is now hosting index and annotation files suitable for Tophat/Cufflinks for several genomes. You can get them here:
http://cufflinks.cbcb.umd.edu/igenomes.html
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Old 06-30-2013, 06:54 PM   #4
windowon
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hi,newcomers ....eager to learn from you
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