Dear Biostars Community,
Im trying to quantify RNAseq data using HTseq-count to get number of reads per gene. In the documentation it says that HTseq by default ignores multimapping reads. But in the manual (https://htseq.readthedocs.io/en/release_0.11.1/count.html) the default for secondary alignments is set to "score" and not "ignore". I don't understand what this means. If it ignores multi mappers by default why is the default parameter for counting multimappers set to "score?"
Also, if I'm not using htseq-count for differential expression analyses but just to look at the expression level of all genes in my model organism, should I include multimapping reads in the gene counts? or not?
Im really confused and would be grateful for your insights on this issue.
Thanks a lot for your help.