Can I use repeatbed from ucsc if my STAR index was built with the gtf file from ensembl?

LosicLab / starchip

Detection of Circular RNA and Fusions from RNA-Seq

http://starchimp.readthedocs.io/en/latest/

MIT License

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Can I use repeatbed from ucsc if my STAR index was built with the gtf file from ensembl? #22

Open shimw6828 opened 5 years ago

shimw6828 commented 5 years ago

I built my star index with the gtf file from ensembl, but I found the repeatbed file was obtained from ucsc. So I don't know if they are compatible in starchip. Do I need to make some changes to repeatbed file? such as chr1 -> 1

kippakers commented 5 years ago

Hi, yes, you will need the chromosome identifiers to be the same, either both with "chr1" or both "1". Other than that, so long as the build is the same (eg. Hg38) it will be just fine.

shimw6828 commented 5 years ago

Hi, yes, you will need the chromosome identifiers to be the same, either both with "chr1" or both "1". Other than that, so long as the build is the same (eg. Hg38) it will be just fine.

Thanks, I have another question。 Should the file in reference be modified?