Go Back   SEQanswers > Sequencing Technologies/Companies > SOLiD

Similar Threads
Thread Thread Starter Forum Replies Last Post
no enrichment of beads --> any ideas why? lichtfaengerin 454 Pyrosequencing 1 08-11-2011 03:45 AM
SizeSelect gel vs Beads wangchy SOLiD 1 02-09-2011 01:59 PM
Calibration beads mestro2 Sample Prep / Library Generation 1 11-30-2010 08:59 AM
mag beads? link1 Sample Prep / Library Generation 1 08-13-2010 07:34 AM
Beads/slide Katsu SOLiD 1 09-22-2009 02:14 PM

Thread Tools
Old 12-19-2011, 03:43 AM   #1
Location: Milano, Italy

Join Date: Aug 2011
Posts: 93
Default Good Beads / Best Beads

We are running a WT Paired End analysis on SOLiD 5500XL. We noticed that the percent of Fraction of Good/Best Beads drops dramatically after each cycle (from 80% to ~ 50%). It should be normal but I would like to know the optimal range for a good run.
Any suggestions??
Attached the box plot of one lane.
Attached Images
File Type: png L02_F5-RNA_PM_boxFracGoodBestBeads.png (25.9 KB, 62 views)

Last edited by paolo.kunder; 12-19-2011 at 08:27 AM.
paolo.kunder is offline   Reply With Quote
Old 03-25-2013, 01:30 AM   #2
Junior Member
Location: india

Join Date: Apr 2012
Posts: 4

We have also done a WT run and are experiencing the same case (starts from around 70 and drops till 30%). I have attached the attached the box plots for both the F5 and the F3 tag. Also when viewing the run in real time the height of the bars decreases with each ligation. Any suggestions ??

Attached Images
File Type: png L01_F3_PM_boxFracGoodBestBeads.png (24.3 KB, 16 views)
File Type: png L01_F5-RNA_PM_boxFracGoodBestBeads.png (25.7 KB, 11 views)
jayalakshmi is offline   Reply With Quote
Old 03-27-2013, 03:12 PM   #3
Junior Member
Location: North America

Join Date: Oct 2012
Posts: 4

The paired end chemistry requires a ligation step which is not as efficient. It's normal to see F5 dropping off quicker than F3. This is/was the cause of many complaints from Solid/5500 users. Life Tech released a number of technical "fixes" to improve the situation but fundamentally F5 never going to be as good as F3.
My take is both these plots are normal performance for the instrument/chemistry.
JackQuist 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 04:10 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO