SEQanswers

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



Similar Threads
Thread Thread Starter Forum Replies Last Post
Bowtie, an ultrafast, memory-efficient, open source short read aligner Ben Langmead Bioinformatics 514 03-13-2020 03:57 AM
Source of duplication in illumina hiseq paired-end reads? amango Bioinformatics 4 01-31-2012 02:55 AM
Average Read Coverage for 454 paired end read data lisa1102 Core Facilities 8 10-18-2011 08:40 AM
pair-end sequencing produces single-end read artifact pparg Bioinformatics 9 03-29-2010 11:15 AM
Read quality filtering for long, PE runs kmcarr Illumina/Solexa 0 07-21-2009 07:07 AM

Reply
 
Thread Tools
Old 11-01-2010, 07:08 AM   #1
terencetate
Junior Member
 
Location: MA

Join Date: Nov 2010
Posts: 4
Default Source of A runs at end of read?

72bp Illumina GAII reads on small RNA library.

The libraries checked out at 110bp by PAGE, with a bit of a smear upwards from here. I gel-purified between 100 and 150 bases from the gel.

Two main problems:

a) The vast majority of the reads do not contain a small RNA insert. The starting material was low (50-400ng) total RNA input, but given that the library size looked good, I was hoping for better.

b) The reads tend to reach the end of the known library sequence, and are then followed by runs of As, and then random nucleotide sequence. The quality scores are low in this region, but is this common for readthrough beyond the end of the library? I would have expected Ns.

Can anyone suggest reasons why the libraries looked to be of appropriate length, but there were no inserts? Are runs of sequence beyond the end of the library product 'real' polynucleic acid, and can they give the false library sizes? Is there a way to remove them.

Thanks for any suggestions...
terencetate 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 06:30 PM.


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