SEQanswers

Go Back   SEQanswers > General



Similar Threads
Thread Thread Starter Forum Replies Last Post
Newbie Question: How to count genome region coverage and CpG sites coverage? illuminaGA Bioinformatics 0 09-25-2015 07:25 AM
Genome in SRA Daniel Fernandez Bioinformatics 0 08-16-2013 10:45 AM
Newbie Question: Calculating physical coverage from genome coverage tristanstoeber Illumina/Solexa 4 06-24-2013 10:53 AM
What does genome-wide coverage look like for good MeDIP/ChIP enrichment? turnersd Bioinformatics 4 08-16-2012 07:31 AM
Adequate coverage for genome wide pair end sequencing Chien-Yuan Chen Bioinformatics 0 03-07-2009 10:49 AM

Reply
 
Thread Tools
Old 02-23-2016, 11:26 AM   #1
jimsac2016
Member
 
Location: Iowa, USA

Join Date: Feb 2016
Posts: 11
Default Genome wide coverage in SRA record

Can one determine the genome-wide coverage of an individual genome deposited in the NCBI SRA database?
jimsac2016 is offline   Reply With Quote
Old 02-23-2016, 12:05 PM   #2
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 6,978
Default

Not unless you align the data. You could calculate theoretical fold representation (based on total number of bases/genome size in bp) but that may not mean much.
GenoMax is offline   Reply With Quote
Old 02-23-2016, 12:09 PM   #3
jimsac2016
Member
 
Location: Iowa, USA

Join Date: Feb 2016
Posts: 11
Default

Thanks, GenoMax. Is there a correlation between low genome coverage and the number of genomic gaps one sees in the alignment with a reference genome? I am trying to make sure that I look at genome-wide coverages of 10 or greater.
jimsac2016 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 02:34 PM.


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