Cufflinks - LOWDATA and NOTEST in *.diff files

szaks

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Join Date: Mar 2013

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Cufflinks - LOWDATA and NOTEST in *.diff files

10-02-2013, 08:25 AM

After running cuffdiff, in all of the *.diff files the test status is “LOWDATA”, “NOTEST”, or, to a smaller extent, “FAIL.” On the other hand, the *_exp.diff files are fine; many of the test status are "OK". Any thoughts why this might be happening?

The LOWDATA status is strange, as all of my targeted genes have >1000x coverage. Of note, this is targeted RNASeq data set; we only sequenced 30 genes. Maybe the targeted nature of the data set is the problem? The .gtf file that I'm using has all human genes in it; should I parse out our targeted genes of interest and use the smaller gtf file?

I'm using cufflinks v2.0.2.

Thanks in advance for any advice, guidance, or direction!
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ramiro2k

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Join Date: Mar 2012

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06-08-2016, 02:32 PM

Any answers?

Did you find a solution to this?? I am experiencing the same problem...
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Cufflinks - LOWDATA and NOTEST in *.diff files

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