I am working on aDNA and I try to simulate some of those reads. So at some point, I have reads into a FastQ file, with qualities, and I run them through Gargammel (a software to simulate aDNA damage). However this software take as input a Fasta file and output another Fasta file with the updated reads.
My question is: I want my FastQ back so, so far, I was using BBMap to go back to Fasta BUT I was putting dummies qualities to all nucleotides of all reads. I wanna know if there is an easy way to recover my previous FastQ qualities and add them to my new created Fasta sequences and create another FastQ file with those sequences and qualities ?
I can do it with by creating my own made script but pretty sure there is an easier/quicker way to do it.
Thanks a lot,