I'm looking to loop through many samples using the bwa sampe command.
Here is what the command looks like for one sample:
bwa sampe ref.fasta read1.sai read2.sai read1.fastq.gz read2.fastq.gz | samtools view -bS - > sample.bam
I have read1.sai, read2.sai, and ref.fasta in the same directory, but not fastq files. I have no problem using a for loop on singleton files. I've tried different things with paired-end reads on the above command but nothing seems to work (I'm not a seasoned programmer). Could someone possibly provide an example for the above command? Apologies if this question is obvious or answered elsewhere.
Here is what the command looks like for one sample:
bwa sampe ref.fasta read1.sai read2.sai read1.fastq.gz read2.fastq.gz | samtools view -bS - > sample.bam
I have read1.sai, read2.sai, and ref.fasta in the same directory, but not fastq files. I have no problem using a for loop on singleton files. I've tried different things with paired-end reads on the above command but nothing seems to work (I'm not a seasoned programmer). Could someone possibly provide an example for the above command? Apologies if this question is obvious or answered elsewhere.
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