SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
How do I find read depth? cnyh RNA Sequencing 0 03-06-2013 04:27 AM
Does the read depth distribution(not read depth) matters yuhao Bioinformatics 0 08-09-2012 05:22 AM
read depth cmccabe Bioinformatics 0 07-19-2012 02:41 AM
Read depth recommendations dpryan RNA Sequencing 2 09-30-2011 11:15 AM
About the read depth of coverage El Mariachi Illumina/Solexa 2 12-30-2010 12:22 AM

Reply
 
Thread Tools
Old 03-08-2013, 08:21 AM   #1
cnyh
Member
 
Location: Norway

Join Date: Feb 2013
Posts: 39
Default How do I find read depth?

With Illumina RNA-Seq data that I've analyzed via TopHat/Bowtie and cufflinks/cuffdiff, what command can I use to find out what the read depth of my samples is?
cnyh is offline   Reply With Quote
Old 03-08-2013, 08:55 AM   #2
jgibbons1
Senior Member
 
Location: Worcester, MA

Join Date: Oct 2009
Posts: 133
Default

You can use samtools depth or samtools mpileup to retrieve coverage values from your mapping output (sorted bam file). You can then sum the depth per site and divide that number by the number of sites in the reference transcriptome.
jgibbons1 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 06:09 AM.


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