Entering edit mode
3.8 years ago
Ada
▴
10
Hello,
What is an appropriate loop for gmap gsnap alignment syntax for ~20K reference genomes? Essentially, I would like gmap gsnap to run through each genome independently and output results?
Like an example loop shown here: A: How to run BWA or the other aligner for paired .fastq in a bash loop and pipelin
You may need to do a nested loop (two
forloops) if you want to align every sample file to every reference.