SEQanswers

Go Back   SEQanswers > Sequencing Technologies/Companies > Illumina/Solexa



Similar Threads
Thread Thread Starter Forum Replies Last Post
Unexpected peaks on Bioanalyzer trace, KAPA hyper prep for ChIP-seq library jpw39 Sample Prep / Library Generation 3 05-11-2016 09:08 PM
Tape Station trace Ben_Niu Sample Prep / Library Generation 3 01-09-2014 01:26 PM
Anyone know what this peak is on my BA trace? Gina_P Sample Prep / Library Generation 4 01-11-2013 12:35 PM
Ideas on Bioanalyzer trace for ChIP-seq library? orlatron Sample Prep / Library Generation 0 05-14-2012 10:02 PM

Reply
 
Thread Tools
Old 03-05-2020, 01:09 PM   #1
Audrey_Sa
Junior Member
 
Location: US

Join Date: Mar 2020
Posts: 1
Question Weird trace in Next-Seq run

Hi,

I have an issue with a recent Next-Seq run and I'm wondering if someone might have any insight. In this run, we pooled together two libraries that were prepared as a customization of the 10x 3' protocol.
The first 25 base pairs seem to be okay, but then there is a stretch of about 75bp of T's. This is not something we were expecting in our library.
I was thinking maybe the adaptor ligation for one of these libraries didn't work, and that possibly messes up the sequencing run? Any other idea would be greatly appreciated since at this point we're not sure what went wrong.
Audrey_Sa is offline   Reply With Quote
Old 03-05-2020, 03:40 PM   #2
luc
Senior Member
 
Location: US

Join Date: Dec 2010
Posts: 446
Default

This is expected. You are sequencing through the poly-A tail. You can ignore this part of the data, and sequence only ~30 (?) cycles for the forward read next time.
luc is offline   Reply With Quote
Old 03-05-2020, 04:02 PM   #3
jdk787
josh kinman
 
Location: Austin

Join Date: Apr 2014
Posts: 69
Default

Quote:
Originally Posted by luc View Post
This is expected. You are sequencing through the poly-A tail. You can ignore this part of the data, and sequence only ~30 (?) cycles for the forward read next time.
Correct, I think 10X says to do 28 cycles for R1, then 8 for i7, then 90 or however many cycles you have left for the insert read in R2
__________________
Josh Kinman
jdk787 is online now   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 05:46 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO