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
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
Manually inspecting? IGV.
More automated...I use coverageBed all the time to check one region versus another.
Leave a comment:
-
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.
best
miroslav
Latest Articles
Collapse
-
by seqadmin
The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...-
Channel: Articles
07-08-2024, 03:19 PM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, Yesterday, 06:46 AM
|
0 responses
9 views
0 likes
|
Last Post
by seqadmin
Yesterday, 06:46 AM
|
||
Started by seqadmin, 07-24-2024, 11:09 AM
|
0 responses
26 views
0 likes
|
Last Post
by seqadmin
07-24-2024, 11:09 AM
|
||
Started by seqadmin, 07-19-2024, 07:20 AM
|
0 responses
160 views
0 likes
|
Last Post
by seqadmin
07-19-2024, 07:20 AM
|
||
Started by seqadmin, 07-16-2024, 05:49 AM
|
0 responses
127 views
0 likes
|
Last Post
by seqadmin
07-16-2024, 05:49 AM
|
Leave a comment: