STARsolo for chimeric reads

[Sogand65]

Hi Alex,

Thanks for the nice package you provided. I have a question, since cellranger does not contain chimeric reads I wanted to know can I use STARsolo and if STARsolo can have the Chimerics and junctions on bam output like the regular STAR does?
I need to find fusion genes on my scRna-seq (10X Genomics) data, and I wanna use the output bam file in Arriba so I can also have the statistic of the fusion genes, do you think I can use STARsolo as instructed in manuscript align with setting that are needed for Arriba as explained below.

I also run regular STAR with passing only fastqs (R2) without containing UMIs to only see if I can STAR+Arriba can find fusion genes, this way is easy for extracting my fusion transcripts only and not for the goal of alignment itselt since STAR can not do demulplexing. Do you think this is a good way just for the sake of detecting fusion transcript only?

Thanks,
Sogi

STAR
--runThreadN 8
--genomeDir /path/to/STAR_index --genomeLoad NoSharedMemory
--readFilesIn read1.fastq.gz read2.fastq.gz --readFilesCommand zcat
--outStd BAM_Unsorted --outSAMtype BAM Unsorted --outSAMunmapped Within --outBAMcompression 0
--outFilterMultimapNmax 50 --peOverlapNbasesMin 10 --alignSplicedMateMapLminOverLmate 0.5 --alignSJstitchMismatchNmax 5 -1 5 5
--chimSegmentMin 10 --chimOutType WithinBAM HardClip --chimJunctionOverhangMin 10 --chimScoreDropMax 30
--chimScoreJunctionNonGTAG 0 --chimScoreSeparation 1 --chimSegmentReadGapMax 3 --chimMultimapNmax 50