Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
TopHat -paired end vs single end reads adarshjose RNA Sequencing 10 06-12-2012 07:15 PM
Can Cuffdiff treat paired-end and single-end reads at the same time? zun RNA Sequencing 3 06-12-2012 06:37 PM
Can paired-end mapping produce more reads than single-end ? warrenemmett Bioinformatics 13 03-21-2012 12:10 AM
Difference in paired-end and single-end read ? darshan Bioinformatics 1 10-01-2009 12:44 AM

Thread Tools
Old 01-02-2013, 04:52 AM   #1
Location: India

Join Date: May 2012
Posts: 130
Default Single end read with paired end reads


I've a few samples whose read 2 has not worked and thus contain only read 1. The same samples have been run again and I got around 20x coverage for these samples (read1 & 2). My question, can I merge the these single reads (only read 1) with the paired end reads in order to increase my coverage of samples? If so, will there be any effect on the results?

tahamasoodi is offline   Reply With Quote
Old 01-16-2016, 04:36 AM   #2
Junior Member
Location: Warsaw, Poland

Join Date: Apr 2013
Posts: 2

Sorry, I guess my post was off topic here after seeing Brian's answer.

Last edited by pawel.osipowski; 01-16-2016 at 10:15 AM.
pawel.osipowski is offline   Reply With Quote
Old 01-16-2016, 08:46 AM   #3
Brian Bushnell
Super Moderator
Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707

I recommend trimming read 2 down to length 1 in the samples that failed. So, read 1 will be full length, read 2 will be length 1, and they will still be paired and correctly ordered; this makes it easy to concatenate the files and map them together. Mappers will ignore length-1 reads.
Brian Bushnell is offline   Reply With Quote

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 10:11 AM.

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