Loop in bwa commands

[Kax]

Hiya,

I'm trying to loop multiple input files with matching prefixes and different file types in bwa sampe ; here's the general structure:

bwa sampe /Users/xxx/Desktop/Index_align/GRCh37_latest_genomic.fna H2_S16_L001_read1.sai H2_S16_L001_read2.sai \
H2_S16_L001_R1_001.fastq.gz H2_S16_L001_R2_001.fastq.gz > aln_H2_S16_L001.sam

I'm trying to make a loop like:

for i in /Users/xxx/Desktop/Index_align/Fastq/fastq_run4/ \
do bwa sampe /Users/xxx/Desktop/Index_align/GRCh37_latest_genomic.fna \
$i\-read1.sai $i\-read2.sai $i\-R1_001.fastq.gz $i\-R2_001.fastq.gz > $i\-aln.sam; done

Does anyone have suggestions for what I am missing? Like perhaps I need to create a list of the prefix file names? I would greatly appreciate any advice. Thanks!

[abedkurdi]

You can do the following:
for f in /Users/xxx/Desktop/Index_align/Fastq/fastq_run4/*.fastq.gz; do
name=$(basename $f _L001_R1_001.fastq.gz)
bwa sampe /Users/xxx/Desktop/Index_align/GRCh37_latest_genomic.fna \
${name}_L001_read1.sai ${name}_L001_read2.sai \
${name}_L001_R1_001.fastq.gz ${name}_L001_R2_001.fastq.gz > ${name}_aln.sam
done