Hi, I am new to RNASeq data analysis but was hoping to use your best practices to look for somatic variants in my data. I have aligned my reads with STAR but now I'm stuck at MergeBamAlignment.
b) What does unmapped.BAM in this context mean?
Am I meant to use the -- outReadsUnmapped of STAR, convert that fastq to BAM and use that alongside my aligned.BAM? Or is it the original BAM file from the sequencer? (To me it sounds like the latter but I just want to double check...) I've tried looking in various forums but have not been able to resolve my doubts and would be grateful for help.
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