Editing
Kun:LabNotes/HiResChrPaint
(section)
Jump to navigation
Jump to search
Warning:
You are not logged in. Your IP address will be publicly visible if you make any edits. If you
log in
or
create an account
, your edits will be attributed to your username, along with other benefits.
Anti-spam check. Do
not
fill this in!
===Barcode design=== *Each barcode has N number of digits, each digit can have M colors. We start with N=7 and M=4. *To better resolve the barcodes, we require that two adjacent digits have different color. Therefore, the total number of possible barcodes is M*(M-1)^(N-1), which is 8748 when N=7 and M=4. *The size of a digit depends on how well we can resolve a feature optically. Based on existing publications, this could be anywhere between 10-400kb. *There could be a spacer between digits, but not necessary as long as two adjacent digits have different colors. *We do need a spacer between two adjacent barcodes in order to know where the first digit is. As a start, the spacer can be twice as large as a digit. *Here is an estimation of number of barcodes and probes needed for the entire human genome. {| {{table}} | align="center" style="background:#f0f0f0;"|'''Digit Size''' | align="center" style="background:#f0f0f0;"|'''# probes/digit''' | align="center" style="background:#f0f0f0;"|'''Digits/barcode''' | align="center" style="background:#f0f0f0;"|'''# barcodes''' | align="center" style="background:#f0f0f0;"|'''Barcode size''' | align="center" style="background:#f0f0f0;"|'''Total region covered''' | align="center" style="background:#f0f0f0;"|'''# probes needed for human genome''' |- | 50,000||400||5||324||350,000||113,400,000||648,000 |- | || ||6||972||400,000||388,800,000||2,332,800 |- | || ||7||2916||450,000||1,312,200,000||8,164,800 |- | || ||8||8748||500,000||4,374,000,000||18,560,000 |- | || || || || || || |- | 100,000||400||5||324||700,000||226,800,000||648,000 |- | || ||6||972||800,000||777,600,000||2,332,800 |- | || ||7||2916||900,000||2,624,400,000||8,164,800 |- | || ||8||8748||1,000,000||8,748,000,000||9,280,000 |- | || || || || || || |- | 200,000||400||5||324||1,400,000||453,600,000||648,000 |- | || ||6||972||1,600,000||1,555,200,000||2,332,800 |- | || ||7||2916||1,800,000||5,248,800,000||4,511,111 |- | || ||8||8748||2,000,000||17,496,000,000||4,640,000 |- | |} *As long as we can resolve individual barcodes, and two adjacent digits have different color, the mapping resolution equals to the size of a digit, not the size of a barcode. *We can also organize the distribution of the barcodes along the entire genome, such that there is a high-level pattern. For example, all barcodes in the same chromosome or chromosome bands can share the same first three digits, similar to how zip codes are designed. This might help us to rescue a barcode that has low/no signals on some digits based on the adjacent barcodes.
Summary:
Please note that all contributions to ZhangLabWiki may be edited, altered, or removed by other contributors. If you do not want your writing to be edited mercilessly, then do not submit it here.
You are also promising us that you wrote this yourself, or copied it from a public domain or similar free resource (see
ZhangLabWiki:Copyrights
for details).
Do not submit copyrighted work without permission!
Cancel
Editing help
(opens in new window)
Navigation menu
Personal tools
Not logged in
Talk
Contributions
Create account
Log in
Namespaces
Page
Discussion
English
Views
Read
Edit
View history
More
Search
Navigation
Main Page
Current events
Recent changes
Random page
Investigators
Matt Cai
Song Chen
Eric Chu
Dinh Diep
Elizabeth Duong
Shicheng Guo
Alan Fung
Daniel Jacobsen
Blue Lake
Huy Lam
Alice Li
Andrew Richards
Brandon Sos
Chris Wei
Yan Wu
Kun Zhang
Tools
What links here
Related changes
Special pages
Page information