Could the documentation be updated to explain what is the effect of omitting --exon and --ss during hisat2-build? For example, will omitting these arguments cause lower mapping rates for RNA-Seq runs, or is it just a question of run-time performance with somewhat equivalent end results?
There's at least one other issue in this repo where users mention not knowing the impact (#162 ), as well as a few external threads on Biostars/other forums (sometimes, with contradicting answers), and the Nature Protocol paper doesn't describe what the outcome of including/omitting them would be, other than the larger memory requirement if included. It would be greatly appreciated if a developer of HISAT2 could add that information in the documentation.
Could the documentation be updated to explain what is the effect of omitting
--exonand--ssduringhisat2-build? For example, will omitting these arguments cause lower mapping rates for RNA-Seq runs, or is it just a question of run-time performance with somewhat equivalent end results?There's at least one other issue in this repo where users mention not knowing the impact (#162 ), as well as a few external threads on Biostars/other forums (sometimes, with contradicting answers), and the Nature Protocol paper doesn't describe what the outcome of including/omitting them would be, other than the larger memory requirement if included. It would be greatly appreciated if a developer of HISAT2 could add that information in the documentation.