Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Agilent SureSelect XT2 pre-capture library construction rthornton4 Sample Prep / Library Generation 1 01-30-2013 06:17 AM
Agilent SureSelect pre-capture multiplexing: which service provider ? carole_smadja Core Facilities 3 11-21-2012 09:14 AM
about Agilent's SureSelect DNA Capture Array chenjy Bioinformatics 2 05-02-2011 08:11 PM
Baits length for exome capture? (Nimblegen and Aglient) sehrrot Sample Prep / Library Generation 3 04-04-2011 02:39 PM
Procedure for paired-end with Agilent SureSelect array capture dnaeve Genomic Resequencing 5 04-16-2010 10:09 AM

Thread Tools
Old 11-05-2012, 06:11 AM   #1
Junior Member
Location: Melbourne

Join Date: Feb 2011
Posts: 6
Default Agilent capture baits

I am setting up targeted sequencing using custom Agilent capture system. The design of the capture baits returned nearly 100,000 probes. The information is provided as BED file. Is there a good way of evaluating the design quality, other than manually inspecting location of 1000s of probes (), before committing to kit production? In particular, the coverage of different loci varies considerably - presumably on account of repeats and perhaps GC content variation (?). What are relative merits of bait boosting vs higher density tiling (1X density vs 2X density)?
Answers and/or pointers to resources appropriate for novices would be gratefully appreciated.
miroslav is offline   Reply With Quote
Old 11-05-2012, 07:00 AM   #2
--Site Admin--
Location: SF Bay Area, CA, USA

Join Date: Oct 2007
Posts: 1,355

Manually inspecting? IGV.

More automated...I use coverageBed all the time to check one region versus another.
ECO is offline   Reply With Quote
Old 11-16-2012, 02:34 AM   #3
Junior Member
Location: Melbourne

Join Date: Feb 2011
Posts: 6
Default capture baits

Thanks ECO for the pointers - slowly getting on top of this.
Is there any resource that could explain benefits of different options in targeted capture probe design? For instance, bait boosting (by Agilent protocol) appears to help with high GC regions and orphan probes but has no effect on target coverage. The probe density appears to have moderate effect on coverage but at a significant cost in terms of number of probes required for the same target as one would expect. I would like to learn how to balance these things but not sure where to start.
Any help would be appreciated
miroslav is offline   Reply With Quote

bedfile, capture baits

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 05:17 AM.

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