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Problem with the --aligner option #6

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daguilarvhio opened this issue Mar 8, 2022 · 0 comments
Open

Problem with the --aligner option #6

daguilarvhio opened this issue Mar 8, 2022 · 0 comments

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@daguilarvhio
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Hi! The documentation contains the line:

python xenosplit.py --out graftOut.bam --aligner star graft.bam host.bam

However, I just downloaded xenosplit (git clone https://github.com/goknurginer/XenoSplit.git) and when I run:

python xenosplit.py --pairedEnd --out output.bam --aligner star RNAtumor.STAR.HUMAN.bam RNAtumor.STAR.MOUSE.bam

I get the following error message:

usage: xenosplit.py [-h] [--count] [--min MIN] [--out OUT] [--pairedEnd]
graft host
xenosplit.py: error: unrecognized arguments: --aligner RNAtumor.STAR.MOUSE.bam

I seems that the current version of Xenosplit does not allow the --aligner option.
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@daguilarvhio