Using Arriba for gene fusion? chimOutTyp SeparateSAMMold of star not working

Question

[Claire]

Hi Everyone

I am trying to use Arriba for gene fusion. Arriba requires either -x parameter, if we use --chimOutType WithinBAM in STAR alignments. or requires -c parameter, if we use --chimOutType SeparateSAMold in STAR alignments.

I used --chimOutType SeparateSAMold in STAR, but nothing was seperatly output. So -c parameter of Arriba fails. I used --chimOutType WithinBAM, Arriba -x parameters fails as well and asked for a separate chimeric file. Has anyone faced this issue?

I am using STAR version 2.7.10a And Arriba 2.2.0

Thanks

[nicolas.ares]

Hi I'm getting the same error, did you find anyway to solve it??

Answer 1

[uhrigs]

Sorry for the late reply. Somehow biostars did not notify me about this post.

1. If you run STAR with --chimOutType SeparateSAMold, you must run Arriba with both -c and -x, because the chimeric reads and the normal reads are distributed over two files (namely, Chimeric.out.sam and Aligned.out.bam).

2. If you run STAR with --chimOutType WithinBAM, then Arriba must be run with -x only.

3. Probably the reason why you got no separate chimeric fine is because you need to use additional parameters, most notably --chimSegmentMin 10.

Please refer to the Arriba user manual for more details. https://arriba.readthedocs.io/