Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Collapsed reads vs overlapping paired-end reads !!?? Patrice Bioinformatics 1 09-08-2016 06:58 PM
Calculating coverage based on full insert size from paired-end data rnaeye Bioinformatics 3 11-09-2015 10:49 AM
Calculating Read/Coverage Depth per Base Pair from a GFF3 File dgosting Bioinformatics 3 10-14-2015 03:57 AM
Tool(s) for calculating depth and genome coverage cheezemeister Bioinformatics 8 04-24-2015 12:29 AM
Overlapping paired end reads in SOAPdenovo Fernando Seixas Bioinformatics 0 11-26-2013 05:40 AM

Thread Tools
Old 04-09-2018, 06:32 AM   #1
Senior Member
Location: US

Join Date: Aug 2011
Posts: 101
Default Calculating depth of coverage for overlapping paired-reads

Hi all,
I have a question on calculating the overall depth of coverage for exome or targeted panel sequencing samples.

As a simple example. If I have paired-end reads that overlap each other. A particular base-pair, would have been sequenced twice, once by the forward read and once by the reverse read. When calculating depth at the base, would you consider this base as having a 1X coverage or a 2X coverage. Essentially treating each individual read of a paired-end as a separate event, or considering them as as combined single event at the base?

lre1234 is offline   Reply With Quote
Old 04-09-2018, 09:28 AM   #2
Registered Vendor
Location: Eugene, OR

Join Date: May 2013
Posts: 453

I think it depends on the precise definition of depth you are using:
read depth-treat them all independently
fragment depth-count overlaps once
de-duplicated read depth-count overlaps once, and remove PCR duplicates, cluster duplicates, etc.
Providing nextRAD genotyping and PacBio sequencing services.
SNPsaurus is offline   Reply With Quote

coverage depth, overlapping paired end, pair end reads

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 02:44 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO