Well you've all been wonderful about answering my novice questions...so here is another. I thank you in advance for generously providing an answer.
What I'm trying to do is loop through a directory, using simple bash script, to a set of files and then process the files to a *.sam format using bwa...here's the code I have so far...
#!bin/bash
#basic syntax below
#bwa samse ref.fa aln_sa.sai short_read.fq > aln-se.sam
module load bwa
FILE1="$WORK/trimmed/*se.fq"
FILE2="$WORK/trimmed/*.sai"
for f in FILE1 and FILE2
do
bwa samse whole_genome.fa "$f2".sai "$f1".fq > "$f".sam
done
What I'm trying to do is loop through a directory, using simple bash script, to a set of files and then process the files to a *.sam format using bwa...here's the code I have so far...
#!bin/bash
#basic syntax below
#bwa samse ref.fa aln_sa.sai short_read.fq > aln-se.sam
module load bwa
FILE1="$WORK/trimmed/*se.fq"
FILE2="$WORK/trimmed/*.sai"
for f in FILE1 and FILE2
do
bwa samse whole_genome.fa "$f2".sai "$f1".fq > "$f".sam
done
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