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*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. | |||
===Probe design=== | ===Probe design=== |
Revision as of 07:19, 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 | ||
- 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.
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>