I have 72 paired end .fastq file for which i need to do Alignment using BWA. Since its a paired end data and my files are named as
sam_002_2.fastq & so on
Since its a paired end data i am not able to generate a single .sam file using a shell script. my script is generating individual .sam file for each .fastq files. Please let me know whats the best strategy for handling this.
EDIT:1 My script
for i in *.fastq; do bwa mem -t 10 /data2/Exome/HG19/BWA/hg19 1.$i 2.$i > /data2/validation_samples/fastq2sam/$i.sam; done