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Old 04-08-2011, 12:23 PM   #1
Location: baltimore

Join Date: Oct 2009
Posts: 89
Default Cufflinks - Nature Biotech data sets


Did any one tested as a practice test the data set that was deposited in GEO. Trapnell et al. deposited data to GEO (GSE20846).

I took that data (sam files and GTF files and ran through the cufflinks (cuffcompare and cuffdiff).

cuffcompare 24.gtf 60.gtf 5d.gtf 7d.gtf

cuffdiff stdout.combined.gtf 24.sam 60.sam 5d.sam 7d.sam

Here cuffcompare output is stdout.combined.gtf (one of the Out put files).

for cuffdiff I gave input combined.gtf and other sam files.

when I check gene_exp.diff file, 6th column that defines the test result (NOTEST, OK, FAIL). In my case the result for this column for every row is NOTEST. that means not enough alignments for testing.

Is there something wrong.

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Old 04-16-2011, 05:40 PM   #2
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Location: Long island

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I think they were using the old version of Cufflinks, cuffcompare cuffdiff etc....are you trying the version when the paper was published?
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