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.
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