How to generate junctions file for star_fusion

Healthcare Parabricks
1

Hi there,

I am trying to run starfusion where it requires the “Chimeric.out.junction” file created by STAR.

When I run the star alignment pipeline with the following command I don’t get the “Chimeric.out.junction” file. is there something I should change?

pbrun rna_fq2bam --ref ../hg19a.fa  --in-fq Z01669_1_lane_dupsFlagged.bam.fq1 Z01669_1_lane_dupsFlagged.bam.fq2 --genome-lib-dir STAR_hg19_ref/ --output-dir rna_fq2bam_out --out-bam rna_fq2bam.bam --out-chim-type Junctions
3

Hello rcorbett1,

we are looking at this right now and will get back to you soon.

Best,
Myrieme

4

Hi rcorbett1,

it seems you did not pass the parameter to get the chimeric output.
Please try again using --min-chim-segment with a value greater than 0.

Best
Myrieme

5

Thanks. That works.

6

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