How to run STAR-WASP mode in pbrun rna_fq2bam?

Healthcare & Life Sciences Parabricks
1

Hello! I want to use parabricks for my RNA seq data with --waspOutputMode & –varVCFfile and cound not able to find any description of WASP mode in pbrun rna_fq2bam –help info. Does anyone tried parabrick’s STAR alignment with WASP mode on?

Thak you :)

2

Hello,

Thanks for reaching out. Right now WASP mode is not supported in Parabricks rna_fq2bam, so please switch to the CPU star for your use case.

If you think this feature is important to you, please let us know so we can put it on the tracker and hopefully have some plan around it in the future.

3

Hi thank you for clearing that up, yes I need WASP mode for allele expression analysis of my samples. I will use conventional STAR for this.

Let me know if this feature becomes available in future in parabricks.

Thanks again!