multiple chimOutType

[been9312]

Hi,

I want to use STAR-fusion and arriba for fusion analysis of RNA sequencing samples.
Both caller use STAR alignment, but the chimOutType files used here are different.
Is there a way to derive both the Junction and the withinBAM HardClip from the --chimOutType at once when turning the STAR alignment?

[alexdobin]

Hi @been9312

yes, you can use --chimOutType Junctions WithinBAM HardClip to simultaneously output chimeras to Chimeric.out.junction and BAM.

Cheers
Alex

[anoronh4]

I am also interested in creating one bam for both STAR-fusion and arriba. I noticed that STAR-fusion recommends --chimMultimapNmax > 0, which only works with --chimOutType Junctions, and when I run with --chimMultimapNmax 1 --chimOutType Junctions WithinBAM HardClip I get the following error:

EXITING because of fatal PARAMETERS error: --chimMultimapNmax > 0 (new chimeric detection) presently only works with --chimOutType Junctions
SOLUTION: re-run with --chimOutType Junctions

Would there be any way to apply --chimMultimapNmax > 0 only the junction output but not to the bam, without running twice?

[alexdobin]

Hi @anoronh4

which version of STAR are using? The latest versions can work for this combination of parameters.

Cheers
Alex