The -M options of cufflinks
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?
1 answer
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.
Log in to answer this question.
More posts like this
-
RNAseq - GBFF cannot be converted to GTF
written by sacdefruits •
-
cufflinks missing some annotations?
written by Sharon
-
Can I use HTSeq-count with a merged.gtf files I created with Cuffmerge?
written by claudia.rivetti85 •
-
Cufflinks de novo assembly, single transcript per gene
written by rnaseq99 •
-
cufflink and cuffmerge error
written by BDK_compbio
-
Cufflinks, without GFF-error
written by milady81
-
Cuffldiff is hanging at "99% complete"
written by M K
-
Why Does Cufflinks With Mask (-M) Option Have Lower Fpkm For Mrna Genes?
written by Xianjun
-
Trouble Linking Gene_Ids From *Gtf File To Assembled Transcripts In Cufflinks
written by User 4409 •
-
Determining Fpkm Of De Novo Assembly Of Transcriptome
written by James Smith •
