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Till now, we only finished read mapping for one sample SAMPLE1. We need to repeat this step for other samples (SAMPL2 - SAMPLE40). You can try something like:
Till now, we only finished read mapping for one sample SAMPLE1. We need to repeat this step for other samples (SAMPL2 - SAMPLE40). You can try something like:
For c shell
foreach file (`ls fastq/SAMPLE*.fastq | cut -f 2 -d '/' | cut -f 1 -d '.'`)
foreach file (`ls fastq/SAMPLE*.fastq | cut -f 2 -d '/' | cut -f 1 -d '.'`)
bin/samtools index bams/$file.bam
bin/samtools index bams/$file.bam
end
end
For bash shell
for file in `ls fastq/SAMPLE*.fastq | cut -f 2 -d '/' | cut -f 1 -d '.'`;
do echo $file;
bin/bwa aln -q 15 ref/human_g1k_v37_chr20.fa fastq/$file.fastq > bwa.sai/$file.sai;
bin/bwa samse -r "@RG\tID:ILLUMINA\tSM:$file" ref/human_g1k_v37_chr20.fa bwa.sai/$file.sai fastq/$file.fastq | \
bin/samtools view -uhS - | bin/samtools sort -m 2000000000 - bams/$file;
bin/samtools index bams/$file.bam;
done
