How to generate junctions file for star_fusion

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

Hello rcorbett1,

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


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.


Thanks. That works.

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