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 11:46 PM
coverageBed usagi Bioinformatics 1 01-23-2012 12:13 PM
coverageBed: command not found ibn.adam RNA Sequencing 6 10-29-2011 03:24 PM
coverageBed: command not found ibn.adam RNA Sequencing 0 10-29-2011 12:34 PM
BEDTools..coverageBed query Siva Bioinformatics 2 08-18-2010 12:10 PM

Reply
 
Thread Tools
Old 06-28-2010, 10:11 PM   #1
jlfmssm
Member
 
Location: Boston

Join Date: Apr 2010
Posts: 14
Smile coverageBed question

I try to run coverageBed like this:
/home/ay55/BEDTools/bin/genomeCoverageBed -ibam 1382_1_sorted.bam -i hg18.bed.sorted -g hg18.genome > hg18_seq.cov.txt

no error at all, but when I open hg18_seq.cov.txt, I got this
read block failed - CheckBlockHeader() returned false
Could not read header type

Any idea?
jlfmssm is offline   Reply With Quote
Old 06-29-2010, 12:39 AM   #2
zee
NGS specialist
 
Location: Malaysia

Join Date: Apr 2008
Posts: 249
Default

I dont think you are giving the program the correct options.

You should only one of either

BAM file as input "-ibam"
or
BED file as input "-i"
zee is offline   Reply With Quote
Old 07-01-2010, 03:58 AM   #3
quinlana
Senior Member
 
Location: Charlottesville

Join Date: Sep 2008
Posts: 119
Default

Quote:
Originally Posted by jlfmssm View Post
I try to run coverageBed like this:
/home/ay55/BEDTools/bin/genomeCoverageBed -ibam 1382_1_sorted.bam -i hg18.bed.sorted -g hg18.genome > hg18_seq.cov.txt

no error at all, but when I open hg18_seq.cov.txt, I got this
read block failed - CheckBlockHeader() returned false
Could not read header type

Any idea?
Assuming you want to run genomeCoverageBed (chromosome level coverage), you would do so as follows:

Code:
genomeCoverageBed -ibam 1382_1_sorted.bam  -g hg18.genome > hg18_seq.genomecov.txt
If you want to run coverageBed (coverage across intervals defined in a BED file):

Code:
coverageBed -ibam 1382_1_sorted.bam -b hg18.bed.sorted  > hg18_seq.cov.txt
I hope this helps,
Aaron
quinlana is offline   Reply With Quote
Reply

Tags
coveragebed

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 10:32 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2017, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO