Hi guys I'm analyzing some high-coverage trio data. So Need to run BWA for hundreds of fastq.gz files. Obviously I should write some script to finish such task without waiting and typing in hundreds of commands one by one. But as a beginner without coding experience, I don't know how to do.
For example, I just put
bwa aln -t 24 index file1>1.sam bwa aln -t 24 index file2>2.sam bwa aln -t 24 index file3>3.sam ............... ..............
into the script, and run it..........and it doesn't work at all. I know I must miss sth., say, the pathway for fastq files.
anyone can give any pattern about such script of executing multiple jobs? thx