Running STAR-SEQR with star outputs

Question

[avelarbio46]

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

[GenoMax]

Even though the project page says

utilize existing outputs from STAR

they have not shown an example of how one would do that. That commands you are trying seem to have no BAM input. So that is likely your problem. If in-line help of the program shows how to provide a pre-aligned BAM file then follow those directions. Try starseqr.py -h or --help and see if you get some assistance.