SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
coveragebed output result problem edge Bioinformatics 2 07-20-2014 10:46 PM
coverageBed: command not found ibn.adam RNA Sequencing 6 10-29-2011 02:24 PM
coverageBed: command not found ibn.adam RNA Sequencing 0 10-29-2011 11:34 AM
BEDTools..coverageBed query Siva Bioinformatics 2 08-18-2010 11:10 AM
coverageBed question jlfmssm Bioinformatics 2 07-01-2010 02:58 AM

Reply
 
Thread Tools
Old 01-20-2012, 03:57 PM   #1
usagi
Junior Member
 
Location: japan

Join Date: Feb 2011
Posts: 4
Default coverageBed

Hi,

Could someone please tell me which column of the output file from "coverageBed" is the number of the raw read count for each gene? Actually, I do not understand the explanation in the protocol.
-------------------------------------------------------------------------------------
Default Output of coverageBed:
After each entry in B, reports:
1) The number of features in A that overlapped the B interval.
2) The number of bases in B that had non-zero coverage.
3) The length of the entry in B.
4) The fraction of bases in B that had non-zero coverage.
-------------------------------------------------------------------------------------
usagi is offline   Reply With Quote
Old 01-23-2012, 11:13 AM   #2
mgogol
Senior Member
 
Location: Kansas City

Join Date: Mar 2008
Posts: 197
Default

If A is the reads and B is the genes, then the last four columns will be # reads per gene, # bases of the gene with reads overlapping them, length of gene, and fraction of gene with reads.
mgogol 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 08:51 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO