Hello, I hope you all well in these times. I am very new in bioinformatics, currently doing pipeline with human diseased and control samples using STAR aligner and I got as an output .bam files. I need to put .bam files into Salmon for quantification and can someone help me to understand how it is done, please? If you can suggest any existing pipeline that I can have a look at how it is done? I generated Salmon index code : salmon index \ -t /Homo_sapiens.GRCh38.cdna.all.fa \ -i SalmonIndex \ -k 31 will appreciate for any advice in STAR-SALMON !