Question: The -M options of cufflinks
gravatar for billzt
5.8 years ago by
billzt20 wrote:

Cufflinks has an option of -M <mask.(gtf/gff)>,  which could be used to mask certain transcripts. However, I still found many transcripts having some levels of FPKM after masking, some even reach ~200 Besides, the file "skipped.gtf" in my output directory is blank!. Obviously, something was wrong with the GTF file I supply for -M option.

How do I generate a suitable file for -M option?

rna-seq cufflinks mask • 1.6k views
ADD COMMENTlink modified 5.8 years ago by Angle4590 • written 5.8 years ago by billzt20
gravatar for Angle45
5.8 years ago by
United States
Angle4590 wrote:

Your best bet is to download a gtf file from Ensembl and test it.  Then, try downloading the same gtf file from an alternate source.  If you are still experiencing a problem from both cases, and the gtf file is identical, the problem probably has nothing to do with your gtf file.

ADD COMMENTlink written 5.8 years ago by Angle4590
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