I have an issue and I'm completely running out of idea here.
I have a fasta file with mutiple sequences. I have an ID file with IDs corresponding to some of the sequences in the fasta file and I want to extract those sequences.
Typical task, I've done it many times either using grep or awk like:
grep -A1 -w -f id_file.txt Input.fasta > output.fasta
Thing is this time, It doesn't work. Even though I can find the ID when using ctrl F look for in notepad. When I used grep or awk it doesn't give me anything. I've suspected hidden character or "to the next line" character issue but none of those were the issue.
Does any of you have an idea on what could prevent grep to recognize my sequences and to extract them?
Thank you very much for any help. Best,