HT-seq-count default parameter to "score"secondary alignments contradicts its documentation that it ignores multi mappers by default. Not clear!

Question

[Zee_S]

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.

[michael.ante]

I guess it's only "scored" if you set the parameter "--nonunique" to "all". Afterwards, you can count the secondary and supplementary alignments.