Hi, I have two fasta files that I want to align together. One (A) contains fragments of a sequence that is created by a sliding window step size of 1. The other one (B) is multiple sequences. I want to align A with B and use the output (can I only get one output?) to label the fragment in A (to show that it was mapped to a sequence in B). I tried to use bowtie 2
but apparently, I have to use a fastq file. I also wanted to try emboss water
but I am not sure if I can use it for multiple sequences for both files.
Is there anyway I can achieve this?
I decided to go with
bowtie2
because I'm more familiar withbowtie
in general. Thank you for the tip about using-f
!