I was wondering if you would have any suggestions as to what options would be recommended for a bacterial RNA-seq. While regular genomic aligners are often used with bacterial data, they don't have the best compatibility with other RNA-seq specific tools, and limit some downstream options.
Right now I'm trying to come up with good settings for bacterial alignment, but don't have a very good idea how to benchmark the results. Any hints would be appreciated.
Hello,
I was wondering if you would have any suggestions as to what options would be recommended for a bacterial RNA-seq. While regular genomic aligners are often used with bacterial data, they don't have the best compatibility with other RNA-seq specific tools, and limit some downstream options.
Right now I'm trying to come up with good settings for bacterial alignment, but don't have a very good idea how to benchmark the results. Any hints would be appreciated.