Pierre Pericard

Beware, this is not just an enhancement but there is a hidden bug in this issue. In compliance with the SAM format specification (http://samtools.github.io/hts-specs/SAMv1.pdf) the 4th column in a SAM...

Yes, that would work when your alignment is nearly global and you dont care about the few soft-clipped nucleotides. It's usually what you get with low-error reads like Illumina's. But,...

Hi @mariabernard , I will let @biocodz or @ekopylova answer you about the future of SortMeRNA. I would just like to point out that, before, when we provided separate databases...

BTW using subcommands would also allow for interesting use cases of SMR if we added a `filter` subcommand, since this is one of the most used function of SMR: ```...

@ekopylova, thanks for your answer. Would it be possible to have more details about these two scores. Since they represent the same alignment there should be a relation between the...

It seems that is not the case. Computing times seems weird however. I need to do more tests.

Hi @EdgarLW, SortMeRNA 4.3.4 is currently integrated in the lastest version of the nf-core/rna-seq pipeline (https://nf-co.re/rnaseq/) and it seems it works well there. Maybe you can have a look at...

Hi @chenyj8, You should probably still use the complete and newer database. If your sample only contains bacteria and archaea then the corresponding rRNA reads will be filtered the same....

Apparently, this was already a bug in SMR v2.1b

I checked, and in BLAST+ the subject coordinates are reversed for reverse-complement matches, not query coordinates. But in DIAMOND (which is closer to what we do in SMR) it is...