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gpertea / stringtie

Transcript assembly and quantification for RNA-Seq
MIT License
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mask file #136

Open zoewardnz opened 7 years ago

zoewardnz commented 7 years ago

Hi,

Apologies if this is in the documentation somewhere. Is there an option in Stringtie to use a mask file (to ignore rRNA, pseudogenes etc?)

Many thanks.

biocyberman commented 6 years ago

@zoewardnz I haven't seen documentation for this neither. But I am working on a similar case, and can tell you something: I mask genome at the before alignment step by using Betools' maskfasta http://bedtools.readthedocs.io/en/latest/content/tools/maskfasta.html. This requires, however, you to index the genome yourself. And it may be impractical for hisat2's high memory usage. Or it may be sufficient to use the -e and -x options. Check them out.