Entering edit mode
5.0 years ago
brunobsouzaa
▴
830
Hello everyone,
I have the following fastq files:
- Sample_1_R1.fastq.gz
- Sample_1_R2.fastq.gz
- Sample_2_R1.fastq.gz
- Sample_2_R2.fastq.gz
- Sample_3_R1.fastq.gz
- Sample_3_R2.fastq.gz
- Sample_4_R1.fastq.gz
- Sample_4_R2.fastq.gz
- Sample_5_R1.fastq.gz
- Sample_5_R2.fastq.gz
I'm wondering if anyone know a perl or bash script that allows me to run BWA-mem simultaneously on those samples. My output has to be:
- Sample_1.sam
- Sample_2.sam
- Sample_3.sam
- Sample_4.sam
- Sample_5.sam
More than one way of doing this in addition to ATpoint 's example below. No perl needed.
BWA mem on multiple samples
Need Coding To Run Bwa Mem In Batch Mode