SEQanswers

Go Back   SEQanswers > Applications Forums > RNA Sequencing



Similar Threads
Thread Thread Starter Forum Replies Last Post
Error using Bowtie alignment mRNA seq ericguo Bioinformatics 2 12-20-2011 10:01 AM
454 Titanium error rate ? 454fungi 454 Pyrosequencing 0 09-14-2010 01:06 AM
error rate der_eiskern Illumina/Solexa 0 12-11-2009 02:51 PM
high first base error rate bioinfosm Illumina/Solexa 4 08-05-2009 02:03 AM
Spikes in error rate by cycle and tile anders Illumina/Solexa 4 10-01-2008 10:08 AM

Reply
 
Thread Tools
Old 05-12-2009, 12:53 PM   #1
Bruce E
Member
 
Location: Rochester,MN

Join Date: Jan 2008
Posts: 15
Default Error rate of 51 cycle mRNA Seq

We have been running mRNAseq on an Illumina GAll. At cycle 36 we are seeing a spike in our error rate. Has anyone else observed this? We do not see it when we run genomic dna or in our standard.
Attached Files
File Type: zip error rate.zip (21.0 KB, 24 views)
Bruce E is offline   Reply With Quote
Old 05-19-2009, 09:25 PM   #2
scbaker
Shawn Baker
 
Location: San Diego

Join Date: Aug 2008
Posts: 84
Default

Bruce,

I have what may be a solution/explanation of your problem, but I'd strongly recommend that you contact Illumina's tech support team as they can help you work through the issue.

Our R&D group used to see higher error rates when they first starting running mRNA-Seq samples longer than 36 reads. It turns out they were sequencing libraries with relatively short inserts (<50 bases). They were reading across the entire insert and in to the adapter sequence on the other side (and since the adapter doesn't align to the genome, you get higher error rates). Libraries with consistently larger inserts are needed when sequencing out to 75 or 100 bases (or beyond). Hopefully this will help you with what you're seeing.

Sincerely,

Shawn C. Baker
Market Manager, Expression and Regulation
Illumina
scbaker 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 03:34 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO