Cufflinks - Nature Biotech data sets

adrian · 04-08-2011, 12:23 PM

Hi:

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.

thanks
Adrian

wuj · 04-16-2011, 05:40 PM

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

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Cufflinks paper published at Nature Biotechnology	Cole Trapnell	Bioinformatics	4	04-17-2011 02:27 PM
Helicos: Yeast Transcriptomics in Nature Biotech	ECO	Helicos / Direct Genomics	0	07-11-2009 01:03 AM
Nature Biotech: Sequencing in real time	mgenome	Literature Watch	0	02-09-2009 08:05 PM
SEQanswers used as a reference in Nature Biotech paper!	ECO	Site Announcements	5	10-26-2008 11:28 PM
Nature Biotech: Next Gen DNA Sequencing Focus	ECO	Literature Watch	0	10-12-2008 07:43 PM

04-08-2011, 12:23 PM	#1
adrian Member Location: baltimore Join Date: Oct 2009 Posts: 89	Cufflinks - Nature Biotech data sets Hi: 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. thanks Adrian

04-16-2011, 05:40 PM	#2
wuj Junior Member Location: Long island Join Date: Jul 2009 Posts: 8	I think they were using the old version of Cufflinks, cuffcompare cuffdiff etc....are you trying the version when the paper was published?