The -M options of cufflinks

Question

[billzt]

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?

Answer 1

[Angle45]

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.