Kun:LabNotes/HiResChrPaint: Difference between revisions
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===Overview=== | ===Overview=== | ||
===Barcode design=== | ===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 | |||
|- | |||
| | |||
|} | |||
===Probe design=== | ===Probe design=== | ||
===Probe synthesis and labeling=== | ===Probe synthesis and labeling=== |
Revision as of 07:12, 17 February 2012
Project threads
Overview
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.
Digit Size | # probes/digit | Digits/barcode | # barcodes | Barcode size | Total region covered | # 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 | ||
Probe design
Probe synthesis and labeling
Hybridization and imaging
Image analysis
Daily Notes
2012 <calendar> name=Kun:LabNotes/HiResChrPaint format=%name/%year-%month-%day date=2012/02/01 view=oneyear </calendar>