Stas Malavin
Stas Malavin
Hi @ahof1704 , ```convertalis``` uses very little resources. I doubt this issue is a memory issue. Actually, error messages in MMSeqs2 are quite uninformative. In my experience, if you get...
Hi Marcel, thanks for the quick reply. Again, I'm sorry for a stupid newbie question. I usually use ```bbmap``` which has a ```minid``` parameter, i.e., 'Approximate minimum alignment identity to...
OK, I think I got the idea. Just to clarify—for the alignments, strobealign has some score threshold, right?
If I use an ```--aemb``` flag, I don't have ```sam``` to filter. Do short alignments show up in the resulting ```tsv```? I actually want to map metagenomic reads to just...
Hi Marcel, thank you very much for the explanations and a helpful discussion! I'll try to update this thread with the results I get using the approach you suggested.
> Minimap2 has a flag (-c I think) which does extension to get the cigar flags added to the PAF format. So, I can just calculate identity from cigar flags...
Great, thanks!