Hi, I am trying to map (short) reads back to metatranscriptome assemblies, but the mapping rate is extremely low for some samples.
I tried to reduce --seedPerWindowNmax as described in e.g. #1414, but it didnt seem to affect the speed at all.
Problematic sample example read stats:
Should I try to reduce --seedPerWindowNmax lower than 30?
Are some of the parameters for indexing or mapping incorrect for the assembly contig/read size/length properties?
Hi, I am trying to map (short) reads back to metatranscriptome assemblies, but the mapping rate is extremely low for some samples. I tried to reduce
--seedPerWindowNmax
as described in e.g. #1414, but it didnt seem to affect the speed at all. Problematic sample example read stats:Index cmd used:
Index log:
Map cmd used:
Log.out
:Log_progress.out
:Should I try to reduce
--seedPerWindowNmax
lower than 30? Are some of the parameters for indexing or mapping incorrect for the assembly contig/read size/length properties?Best
Oskar