Find mean read length of a bam file dataset of reads?
1
0
Entering edit mode
11 days ago
MobiusT • 0

I am working in a remote linux server and I have a dataset of reads in the file with extension bam extension. How to find its mean read length

bam dataset read gz linux • 177 views
ADD COMMENT
0
Entering edit mode

vcfs don't usually contain read length information

ADD REPLY
2
Entering edit mode
11 days ago

you can get the mean read length from a bam or a fastq file, not from a VCF.

ADD COMMENT
0
Entering edit mode

Then, How to find from a bam file?

ADD REPLY
1
Entering edit mode

samtools stats in.bam | grep "average length"

ADD REPLY

Login before adding your answer.

Traffic: 795 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6