Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
minimum and maximum CNV size by Read Depth? eleven Bioinformatics 2 05-29-2013 02:36 AM
minimum depth of coverage for transfrag extension apadr007 Bioinformatics 6 05-15-2012 07:23 AM
Maximum possible coverage depth junfeng Bioinformatics 1 01-18-2012 09:54 AM
What's maximum depth and minimum depth? slny Bioinformatics 0 03-17-2011 11:13 AM
Depth of coverage variation in RNA Seq jay RNA Sequencing 19 08-12-2010 12:26 AM

Thread Tools
Old 07-05-2017, 06:44 AM   #1
Junior Member
Location: Rome

Join Date: Feb 2017
Posts: 3
Default Minimum (ir maximum) bam depth/coverage for structural variation analyses

*or maximum

We are studying structural variation in several plant genomes Illmumina pair-end DNA re-sequencing, and noticed that the number of deletions in some samples (PINDEL) drops significantly. After having boldly calculated the depth as

[number of reads] x mean read length / genome size

we noticed that in these samples the depth was way lower (around 10 folds on an average of 50).

I was wondering if there is some lower or higher limit in a sample depth to start considering an adulterated result.

linudz is offline   Reply With Quote

coverage, depth, illumina, pairend, structural variation

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 11:38 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO