Convert bam files to pair-end FASTQ

/software/samtools/1.8/bin/samtools bam2fq -N AGG0011.bam > AGG0011.fastq

cat AGG0011.fastq | grep ‘^@.*/1$’ -A 3 –no-group-separator > AGG0011_R1.fastq
cat AGG0011.fastq | grep ‘^@.*/2$’ -A 3 –no-group-separator > AGG0011_R2.fastq