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Running STAR-SEQR with only star alignment outputs #29

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GACGAMA opened this issue Aug 24, 2021 · 0 comments
Open

Running STAR-SEQR with only star alignment outputs #29

GACGAMA opened this issue Aug 24, 2021 · 0 comments

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@GACGAMA
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GACGAMA commented Aug 24, 2021

Hello!
I've been trying to run STARSEQR with reads already aligned (with options for arriba, star-fusion and STARSEQR).
When running with the following options:

starseqr.py -sb -sj -p -t 8 -g -r --v
or
starseqr.py -sj -sb ​-p -t 8 -g -r --v
or
starseqr.py -sb -p -t 8 -g -r --v
I'm always getting:

starseqr.py: error: the following arguments are required: -1/--fastq1, -2/--fastq2

How can I run the fusion caller only with bam files and chimeric junctions?

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