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huangyh09 / briekit

Preprocessing tool kit of BRIE project in splicing analysis
https://brie.readthedocs.io/en/latest/briekit.html
Apache License 2.0
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briekit with ensembl gtf #7

Open TdzBAS opened 1 year ago

TdzBAS commented 1 year ago

HI,

thanks for this nice tool. When I dont use Gencode gtf, I encounter errors. for GRCh38.p13 from ensembl I get following error:

image

I already added chr as a prefix for the chromosome column, but still the same error.

Any suggestions?

huangyh09 commented 1 year ago

Can you check that both your GTF and FASTA files have the same format of chromosome IDs, e.g., chrX (not X)? Also, it only supports Python 2.

Yuanhua