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YeoLab / outrigger

Create a *de novo* alternative splicing database, validate splicing events, and quantify percent spliced-in (Psi) from RNA seq data
http://yeolab.github.io/outrigger/
BSD 3-Clause "New" or "Revised" License
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How to use outrigger index with "-c"? #94

Open QijinYin opened 4 years ago

QijinYin commented 4 years ago

Hi, I'm going to use outrigger to analysis the GTEx data.

I got the junction read counts file from https://gtexportal.org/home/datasets#filesetFilesDiv13, named "GTEx_Analysis_2017-06-05_v8_STARv2.5.3a_junctions.gct.gz".

Since I have read counts file, I use

outrigger -index -c XX.gct GTEx_Analysis_2017-06-05_v8_STARv2.5.3a_junctions.gct.gz -g XXX

but get the error "KeyError: 'junction_id'"

Is there any demo using junctions read counts as input? or what's the format of the read counts file that outrigger can process?

Thanks a lot!