SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
extract forward and reverse reads? JenBarb RNA Sequencing 26 03-02-2015 08:42 AM
CAP3 for forward and reverse reads sp24 Bioinformatics 4 07-04-2013 02:52 PM
Forward and reverse reads in NGS tahamasoodi Bioinformatics 11 03-12-2013 09:56 AM
forward and reverse reads with BWA jwhite Bioinformatics 3 02-20-2013 09:41 AM
MetaSim: why paired end reverse read is much shorter than forward read?? gen_argentino Bioinformatics 0 09-06-2012 07:38 AM

Reply
 
Thread Tools
Old 10-29-2017, 06:52 PM   #1
DanielSai
Junior Member
 
Location: Australia

Join Date: Oct 2017
Posts: 3
Default Shorter forward reads than reverse

Hello,
I'm DanielSai from Australia.

I did a next gen run on my sample using the illumina miseq machine. I'm getting shorter forward sequence reads than the reverse reads. What could be the problem and how can it rectified in subsequent runs?
DanielSai is offline   Reply With Quote
Old 10-30-2017, 02:20 AM   #2
nucacidhunter
Jafar Jabbari
 
Location: Melbourne

Join Date: Jan 2013
Posts: 1,182
Default

You have not given much details but one reason would be sequencing configuration for example, R1 was set to less cycles than R2.
nucacidhunter is offline   Reply With Quote
Old 10-30-2017, 04:51 AM   #3
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 6,800
Default

There is no logical reason (other than an assymetric run setup mentioned by @nucacidhunter) to get shorter R1 reads compared to R2. What kind of sequencing are you doing and what is the run setup?
GenoMax is offline   Reply With Quote
Old 10-30-2017, 07:35 AM   #4
kmcarr
Senior Member
 
Location: USA, Midwest

Join Date: May 2008
Posts: 1,153
Default

Have the reads been trimmed?
kmcarr is offline   Reply With Quote
Old 10-30-2017, 07:54 AM   #5
DanielSai
Junior Member
 
Location: Australia

Join Date: Oct 2017
Posts: 3
Default

Quote:
Originally Posted by kmcarr View Post
Have the reads been trimmed?
Yes, reads have been trimmed
DanielSai is offline   Reply With Quote
Old 10-30-2017, 08:20 AM   #6
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 6,800
Default

Quote:
Originally Posted by DanielSai View Post
Yes, reads have been trimmed
Then it is odd that only R1 was trimmed (or trimmed to a larger extent than R2). If you have short inserts (and thus read-through into adapters on other end) then R2 reads should also be trimmed to a similar extent.

You still need to address questions in other comments above.
GenoMax 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 03:14 AM.


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