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

Similar Threads
Thread Thread Starter Forum Replies Last Post
polyA containing reads in RNA-seq wenhuang Bioinformatics 6 02-19-2015 04:16 PM
common reasons for failed barcode reads? bombardior Illumina/Solexa 11 01-29-2015 01:43 PM
Only 10% of the RiboZero RNA-Seq reads are from polyA+ RNAs? woodydon RNA Sequencing 1 07-27-2014 01:59 AM
PolyA removal from RNA seq Illumina reads figo1019 Illumina/Solexa 2 11-18-2012 06:06 PM
PolyA reads are disappeared? SOLiDrobino SOLiD 5 08-09-2011 06:24 AM

Thread Tools
Old 03-14-2018, 05:19 AM   #1
Junior Member
Location: Pheonix

Join Date: Mar 2018
Posts: 1
Default Reasons for polyA in RNA Seq Reads

In my poly A capture RNA sequencing fastq output, I noticed that about 20% of the reads contain poly A in the middle (or even close to the front). I would like to understand more on this, because with DNA fragments mostly >300bps and read length 100 bps, we were not expecting to see poly A show up that frequently in reads. I would appreciate your thinking.

To my understanding, even it is a poly A capture sequencing, during the library preparation, the mRNA tail fragments (with polyA) are the only fragments will be selected. In this selection, adapter contains ~15bps poly T can bind anywhere on the polyA tail, which can be >200bps long. My theory is that, if it binds towards the 3' end of polyA, then that literally allows major part of the polyA tail gets amplified in PCR, and can potentially pass size selection, but the coding region in this case can be short at 5'.





Say the Ts-Adapter start binding at the highlighted A, then the last 2-3 A will be gone after first round of pcr, but the rest of As will remain till sequencing.

Any advise is appreciated. Thank you.
DVA is offline   Reply With Quote
Old 03-14-2018, 06:31 PM   #2
Jafar Jabbari
Location: Melbourne

Join Date: Jan 2013
Posts: 1,189

It will be useful if you can give more information on library prep method or kit to narrow on possible causes.
nucacidhunter 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 04:19 PM.

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