Hello,

I am using kallisto genomebam to create bam files. However, I have been trying to figure out how it handles multi mapped reads but I have not been able to understand that. The command that I use looks like:

kallisto quant -i hsGRCh38_kallisto -o folder -b 100 --rf-stranded
--genomebam --gtf Homo_sapiens.GRCh38.96.gtf --chromosomes chrNameLength.txt R1_001.fastq.gz R2_001.fastq.gz

Thank you