Go Back   SEQanswers > Sequencing Technologies/Companies > SOLiD

Similar Threads
Thread Thread Starter Forum Replies Last Post
How to assign values to size factor (DESeq) kentnf Bioinformatics 4 01-14-2014 11:48 PM
Good Beads / Best Beads paolo.kunder SOLiD 2 03-27-2013 02:12 PM
How does Cuffdiff assign p-value when it detects differentially splicing? zhixingfeng Bioinformatics 7 06-21-2012 06:11 AM
How to assign more CPU cores to terminal on Mac? harrike General 1 04-14-2011 09:56 AM
assign chromosome location to gene id rdu Bioinformatics 0 02-10-2011 03:48 PM

Thread Tools
Old 11-06-2010, 07:24 AM   #1
Junior Member
Location: Japan

Join Date: Jul 2010
Posts: 1
Unhappy Does anybody trouble for the number of assign beads ?

Hi all,

I use SOLiD4 , its protocol is Multiplex(barcode) Frangment run.
Usually my sample is ChIP sample.

Though I amplificated 12 libraries and run as usual last time, 4 of 12 libraries were little assign. The number of 4 was ten times or more as little as that of others.
Of course I checked amout of P1-P2fragment by qPCR and collect libraries same range by e-gel.
After I did ePCR using same amout of libraries as a template, I got good results in WFA.

Does anybody know such a trouble?

I have no idea but there is a possibility that the quality of ChIP DNA was bad.
However I cehcked those libraries has P1 and P2 by qPCR and size range was collect.(All libraries were same range.)
Nevertheless, after sequencing the number of assign beads was much different. I couldn't understand.

Other possiblity is the sequence of barcode?? One barcode is easy to assign???

Sorry, but please help me...
Yuki is offline   Reply With Quote
Old 11-07-2010, 05:45 AM   #2
Senior Member
Location: SEA

Join Date: Nov 2009
Posts: 197

How are u assigning the reads?
I had the same prob in 3 plus. Due to multiple reasons.

I used wrong library in setup. ( check if majority of reads are in a particular barcode.

Did u allow 1 mismatch?

Check w ur FAS if there's a better hamming sphere file.
KevinLam 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 10:42 PM.

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