SEQanswers

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



Similar Threads
Thread Thread Starter Forum Replies Last Post
Cluster Radius Info in GAII/HiSeq som_seq Webinar Series 0 08-07-2014 04:04 PM
De Novo Assembly - Illumina GAII & HiSeq 2000 Data milo0615 Bioinformatics 2 05-09-2014 05:02 PM
Your optimum cluster density on a HiSeq? pmiguel Illumina/Solexa 2 07-10-2013 08:22 AM
scaffolding GAII paired-end library with Hiseq mate-pairs stevebaeyen Bioinformatics 17 02-27-2013 02:45 AM
Chemistry and protocol differences in Miseq, GAII and Hiseq? dwang Illumina/Solexa 3 02-19-2013 09:49 AM

Reply
 
Thread Tools
Old 08-07-2014, 04:13 PM   #1
som_seq
Junior Member
 
Location: TX, United States

Join Date: Apr 2014
Posts: 3
Post Cluster Radius Info in GAII/HiSeq Illumina platform

Hello GAII/HiSeq users,

Can someone tell me what is the typical radius of a cluster in Illumina GAII/HiSeq platform? I believe the total number of bridge amplification cycles (~35) has something to do with the area of the cluster, and assuming clusters are roughly circular in shape, radius (or equivalent) will depend on it. Basically, I am trying to find out, given a cluster density/concentration, how close can any two clusters lie, before there is significant overlap between them resulting in failing filters and poor Q scores? I scoured the net for this info but couldn't get one. Would really appreciate if anyone has any pointers to share.

Cheers and have a great day !
som_seq is offline   Reply With Quote
Old 08-07-2014, 05:52 PM   #2
ScottC
Senior Member
 
Location: Monash University, Melbourne, Australia.

Join Date: Jan 2008
Posts: 246
Default

I'm not sure of the raidus, but the stats for optimal cluster densities are already available from Illumina and most labs that run the instruments for a while do have an idea of the optimal densities (from accidental under- and over-clustering that inevitably happens from time to time).

The software that reads the clusters is able to 'section' them to rescue slightly overlapping clusters. Of course, this doesn't work if there are too many clusters all overlapping each other.

Lastly, for a more direct answer to your question... have you asked Illumina?

Cheers,

Scott.
ScottC is offline   Reply With Quote
Old 08-07-2014, 07:40 PM   #3
som_seq
Junior Member
 
Location: TX, United States

Join Date: Apr 2014
Posts: 3
Post

Hi Scott,

Thanks for the reply. However, I am not sure if I understood when you say "the software ... is able to section them..". Do you mean there exists some threshold cluster density above which the overlap phenomenon can be quantified as 'significant' (e.g. % of clusters having x% overlap or more, etc.) ?

I did reach out to Illumina on this, but they were unable to provide details, saying this information falls under "Illumina proprietary" standard.
som_seq is offline   Reply With Quote
Old 08-07-2014, 08:12 PM   #4
ScottC
Senior Member
 
Location: Monash University, Melbourne, Australia.

Join Date: Jan 2008
Posts: 246
Default

No, I mean that the software doesn't necessarily look at a circular cluster. It can take a section through the middle of a cluster, avoiding the edges, to 'rescue' overlapping clusters that may have mixed signals at the edges.

This talks about it very briefly:

http://lhmg.amu.edu.pl/text/sequenci...20analysis.pdf

If you really do need to know the size of a cluster, then you could probably estimate it by measuring it from a cluster images.

Cheers,

Scott.
ScottC is offline   Reply With Quote
Reply

Tags
cluster formation, cluster identification, gaii, hiseq, illumina

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 04:22 AM.


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