Off topic:How to loop over multiple files for BWA MEM in bash for loop?
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Entering edit mode
15 months ago
DNAngel ▴ 120

Hi all,

I've written a large bash script for single-end paired reads which uses bwa mem. It works great. But now I have a new dataset that is paired-end and the only part I need to change is the beginning where bwa mem uses a reference file and sample files to align them. I cannot figure out how to edit my for loop to allow this.

All my sample files have a forward_R1 while and a reverse_R1 file as they are paired files.

My regular bwa mem loop in bash is:

#!/bin/bash
REF=$1 ID=$2

for files in *.fastq
do
bwa mem -B 2 -M-t 40 $REF$files > {files%%.fastq}_aln.sam done  How do I edit this so that it can take two files for the program, but still output the one aligned file? I tried: #!/bin/bash REF=1
ID=$2 for forfiles, revfiles in *.fastq do bwa mem -B 2 -M -t 40$REF $forfiles$revfiles > \${forfiles%%.fastq}_paired_aln.sam
done


But this gives an error because the loop doesn't understand two arguments.

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