Hey everybody!
Just wanted to quickly ask to understand if, by default, all output filtering rules described in the manual are applied?
Example:
I want to align 50bp reads from an RNAseq experiment to the reference genome. Among many others, there are these two rules for output filtering:
--outFilterMismatchNmax [int, default "10"]
alignment will be output only if it has no more mismatches than this value
--outFilterMismatchNoverLmax [float, default "0.3"]
alignment will be output only if its ratio of mismatches to mapped length is less than or equal to this value
Does that mean that in theory a total of 10 mismatches would be allowed per read, but since the reads are only 50 bp long the second rule will reduce that limit to a maximum of 1 tolerated mismatch (50 * 0.03 = 1.5) per read?
I hope I understood that correctly.
Thanks,
Roman