SEQanswers

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



Similar Threads
Thread Thread Starter Forum Replies Last Post
CummeRbund - show individual k-means cluster plots dacotahm RNA Sequencing 1 12-06-2016 10:30 AM
Oxford Metrics jtotheulie Oxford Nanopore 1 05-16-2016 01:02 AM
Newbler Metrics Narmneung Bioinformatics 1 10-23-2014 04:47 AM
What is the meaning of repeat cluster and unique cluster? seungchul Lee Bioinformatics 0 04-12-2014 11:29 PM
v3: Effect of high cluster densities on cluster PF and %Q30 pmiguel Illumina/Solexa 3 10-05-2011 05:36 AM

Reply
 
Thread Tools
Old 02-05-2017, 08:57 AM   #1
garwuf
Junior Member
 
Location: Russia

Join Date: Mar 2009
Posts: 7
Default Cluster metrics for individual barcodes

Hi all,

I wonder if it is possible to assess some useful cluster metrics (FWHM or %>=Q30) not for the entire loaded pool but for individual barcodes (or maybe even for separate reads)? The Illumina SAV can show such stats for particular lanes/tiles but does not track the barcodes. In principle, each read can be tracked back to its location in the flow cell by coordinates extraced from the read name, but is there a way to relate it to a particular cluster and get its size?
garwuf is offline   Reply With Quote
Old 02-05-2017, 09:29 AM   #2
dpryan
Devon Ryan
 
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,474
Default

In the "stats/" directory produced by bcl2fastq you can find an XML file with per-tile metrics on %>=Q30 separated by barcodes.
dpryan is offline   Reply With Quote
Old 02-05-2017, 09:45 AM   #3
garwuf
Junior Member
 
Location: Russia

Join Date: Mar 2009
Posts: 7
Default

Quote:
Originally Posted by dpryan View Post
In the "stats/" directory produced by bcl2fastq you can find an XML file with per-tile metrics on %>=Q30 separated by barcodes.
Thanks a lot, I completely forgot about it.

Last edited by garwuf; 02-05-2017 at 10:16 AM. Reason: typo
garwuf 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 02:00 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2017, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO