SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
edgeR: how to calculate group average/means ? miaom RNA Sequencing 4 08-28-2018 07:06 AM
how to calculate genome coverage correcting for multiple genome hits alice.lunardon Bioinformatics 0 04-30-2013 02:03 AM
How do calculate % of genome with >20x coverage? SeqVicious Bioinformatics 5 08-09-2012 03:56 AM
How to get average coverage from BAM files? Martino Bioinformatics 2 05-11-2012 07:44 AM
how to calculate average gap size odoyle81 Bioinformatics 10 01-20-2012 09:01 AM

Reply
 
Thread Tools
Old 06-02-2014, 09:30 AM   #1
prs321
Member
 
Location: US

Join Date: Jun 2013
Posts: 96
Default How do I calculate the average coverage of genome?

Say if I have an ancestral strain, as well as 20 replicates. The 20 replicates are divided into 4 treatment groups, so 5 replicates per treatment group.

I have 4 .bam files for each treatment group containing 5 replicates per .bam file.

I also have the variant files.

How do I calculate the average coverage of the genome?

I'm confused on what file to use to calculate the average.

Do I use one of my treatment .bam files, a variant file, or the ancestral strain?

I have bedtools installed as well as genomecov, but I'm not sure how to obtain the average coverage value that I am looking for.
prs321 is offline   Reply With Quote
Old 06-02-2014, 06:48 PM   #2
mikep
Member
 
Location: Singapore

Join Date: Feb 2011
Posts: 45
Default

samtools idxstats will give you the number of mapped reads per reference, you can then divide this number by the length of the reference to get the coverage.

Do it for each bam file.
mikep is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 10:23 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO