How to generate a mask gtf for use with cufflinks

Question

[Michelle M.]

Hi all,

I fear that I am missing something incredibly obvious because I can't find any similar questions/answers to this. But any help will be appreciated. How do I generate my mask gtf? I realise I can go to UCSC Genome Browser and export such a file, but I'd prefer to generate my own that is consistent with the specific ENSEMBL gtf that I am using. I've been able to filter this gtf in R according to Mt_rRNA, Mt_tRNA, and rRNA biotypes, but this misses all the tRNA because they aren't assigned to a biotype. I'm using Ensembl Homo_sapiens.GRCh37 gtf file from iGenome.

Any thoughts?

Many thanks, M.

[umn_bist]

By chance, have you looked here https://ccb.jhu.edu/software/tophat/igenomes.shtml?

[Michelle M.]

Hi umn_bist, thanks for the response. Yes, that is where I sourced my complete Ensembl GTF file for GRCh37. Are you suggesting there's a mask gtf also included in that package? Thanks again for your help.