Question: The -M options of cufflinks
0
gravatar for billzt
4.5 years ago by
billzt20
Australia
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 • 1.4k views
ADD COMMENTlink modified 4.5 years ago by Angle4590 • written 4.5 years ago by billzt20
0
gravatar for Angle45
4.5 years ago by
Angle4590
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 4.5 years ago by Angle4590
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1290 users visited in the last hour