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!
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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