Running STAR-SEQR with star outputs

Running STAR-SEQR with star outputs

0

Hello everyone!
I’ve been trying to run STARSEQR with reads already aligned from STAR with specific fusion options. I want to run STAR-SEQR with aligned reads because I’m using these reads for arriba, star-fusion and STARSEQR. If I had to align them for each program, it would take very long as I have >200 samples

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

My question is: How can I run the fusion caller only with bam files output from STAR?

Any suggestions are appreciated


STAR-SEQR


STAR


fusion


RNAseq

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