Entering edit mode
18 months ago
Mgs3 ▴ 30
I understand that for filtering reads based on length i can simply use:
samtools view -h file.bam | awk 'length($10) > 50 || $1 ~ /^@/' | samtools view -bS - > output.bam
But how can i select paired reads that both are longer than 50?
Untested but may also work. Using BBMap suite.