Hi, I have a FASTA file that contains sequences from a de novo assembly. We have identified rRNA sequences that we are now trying to remove from that FASTA file. I can remove lines with sed but have to do it per line in a script and I have about 500 sequences that I need to remove. Is there a way that I can write this to take the matching sequences from file B (the rRNA sequences) and remove them and the line following (the actual sequence in the FASTA file) from file A? I have tried grep and comm but grep gives me a byte error and comm didn't make any difference to my files.
Any guidance would be greatly appreciated.