Hello,
I wanted to know if it's possible to add in your code something to extract the reads mapped.
For instance, I'm only interested to extract E. coli reads that mapped to my E. coli database in a metagenome readset. I'm using Kraken2 for now but have a lot of false positive.
We could imagine something that create a folder according to the name of the strain in the database and put each reads with MAPQ=60 inside.
Thank you for this great tool,
Fabien
Hello, I wanted to know if it's possible to add in your code something to extract the reads mapped. For instance, I'm only interested to extract E. coli reads that mapped to my E. coli database in a metagenome readset. I'm using Kraken2 for now but have a lot of false positive. We could imagine something that create a folder according to the name of the strain in the database and put each reads with MAPQ=60 inside. Thank you for this great tool, Fabien