filter bam file

Question

[hana]

Hi

I have merged bam file which has 24-101 bp reads. I would like to find the alternative splice events using MISO. I need to filter the reds in my merged bam file and keep only reads with 100 bp length. Is there any way to do that?

Thanks in advance

Answer 1

[monica.abrudan]

samtools view -h my.bam | awk '{if($0~/^@/ || length($10) == $Desired_length){print $0}}' | samtools view -bS - > my_new.bam

Answer 2

[Asaf]

Try: samtools view -m 100