Hello everyone, I’m trying to find if a sequence in my multifasta files is present in E. coli.
My multifastafiles looks like this :
It contains around 5000 sequences
I have tried to use mapping tools such as bowtie2, minimap2 but it always tells me that I have 0 sequences that can align on the genome of E. coli, but I know that the sequence “16” is a sequence found in E. coli. So I think that the “N” are the problem, but I don’t know how to overcome it? Is there some parameters that I should change ? Or am I using the wrong tool?