search

suhrig / arriba

Fast and accurate gene fusion detection from RNA-Seq data
Other
224 stars 50 forks source link

Arriba's STAR parameters: is HardClip in "--chimOutType WithinBAM HardClip" required? #173

Closed toddajohnson closed 1 year ago

toddajohnson commented 1 year ago

Hi Sebastian,

Is "HardClip" required for chimeric reads output in the STAR aligned bam file, or is it OK to use "SoftClip" in the --chimOutType? I have been using STAR aligned bam files with softclipped reads in order to see the breakpoints in IGV, but I thought that I should check and make sure that nothing unexpected might be happening under the hood with respect to Arriba's fusion detection.

Thanks, Todd

suhrig commented 1 year ago

Hi Todd,

It makes no difference whatsoever. You can use whatever you prefer.

Regards, Sebastian

toddajohnson commented 1 year ago

Thank you for the clarification!