Alice:LabNotes/2007-12-5: Difference between revisions
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>Zsakura2 No edit summary |
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Sample 1<br> | Sample 1<br> | ||
[[Image:SNP 1.png]]<br> | [[Image:SNP 1.png]]<br> | ||
{| {{table}} | |||
| align="center" style="background:#f0f0f0;"|'''Sample''' | |||
| align="center" style="background:#f0f0f0;"|'''peak location''' | |||
| align="center" style="background:#f0f0f0;"|'''base pair''' | |||
| align="center" style="background:#f0f0f0;"|'''base pair''' | |||
| align="center" style="background:#f0f0f0;"|'''peak value''' | |||
|- | |||
| ZL1-cust.ab1 ||92 ||N ||C ||255 || | |||
|- | |||
| ZL1-cust.ab1 ||94 ||C ||C ||695 || | |||
|- | |||
| ZL1-cust.ab1 ||92 ||N ||T ||214 || | |||
|- | |||
| ZL1-cust.ab1 ||93 ||T ||T ||613 || | |||
|- | |||
| | |||
|} | |||
peak ratio: 255+695 : 214+613 = 950 : 827 <br> | |||
Sample 2<br> | Sample 2<br> | ||
[[Image:SNP 2.png]]<br> | [[Image:SNP 2.png]]<br> | ||
{| {{table}} | |||
| align="center" style="background:#f0f0f0;"|'''Sample''' | |||
| align="center" style="background:#f0f0f0;"|'''peak location''' | |||
| align="center" style="background:#f0f0f0;"|'''base pair''' | |||
| align="center" style="background:#f0f0f0;"|'''base pair''' | |||
| align="center" style="background:#f0f0f0;"|'''peak value''' | |||
|- | |||
| ZL2-cust.ab1 ||96 ||A ||G ||190 || | |||
|- | |||
| ZL2-cust.ab1 ||94 ||G ||G ||724 || | |||
|- | |||
| ZL2-cust.ab1 ||96 ||A ||A ||209 || | |||
|- | |||
| ZL2-cust.ab1 ||95 ||A ||A ||647 || | |||
|- | |||
| | |||
|} | |||
peak ratio: 190+724 : 209+647 = 914 : 856 <br> | |||
Sample 4<br> | Sample 4<br> | ||
[[Image:SNP 4.png]]<br> | [[Image:SNP 4.png]]<br> | ||
{| {{table}} | |||
| align="center" style="background:#f0f0f0;"|'''Sample''' | |||
| align="center" style="background:#f0f0f0;"|'''peak location''' | |||
| align="center" style="background:#f0f0f0;"|'''base pair''' | |||
| align="center" style="background:#f0f0f0;"|'''base pair''' | |||
| align="center" style="background:#f0f0f0;"|'''peak value''' | |||
|- | |||
| ZL4-cust.ab1 ||88 ||C ||C ||763|| | |||
|- | |||
| ZL4-cust.ab1 ||89 ||C ||C ||731|| | |||
|- | |||
| ZL4-cust.ab1 ||88 ||C ||T ||58|| | |||
|- | |||
| ZL4-cust.ab1 ||87 ||T ||T ||475|| | |||
|- | |||
| | |||
|} | |||
peak ratio: 763+731 : 58+475 = 1494 : 533 <br> | |||
Sample 5<br> | Sample 5<br> | ||
[[Image:SNP 5.png]]<br> | [[Image:SNP 5.png]]<br> | ||
{| {{table}} | |||
| align="center" style="background:#f0f0f0;"|'''Sample''' | |||
| align="center" style="background:#f0f0f0;"|'''peak location''' | |||
| align="center" style="background:#f0f0f0;"|'''base pair''' | |||
| align="center" style="background:#f0f0f0;"|'''base pair''' | |||
| align="center" style="background:#f0f0f0;"|'''peak value''' | |||
|- | |||
| ZL5-cust.ab1 ||87 ||T ||T ||386|| | |||
|- | |||
| ZL5-cust.ab1 ||86 ||T ||T ||342|| | |||
|- | |||
| ZL5-cust.ab1 ||87 ||T ||C ||161|| | |||
|- | |||
| ZL5-cust.ab1 ||88 ||C ||C ||583|| | |||
|- | |||
| | |||
|} | |||
peak ratio: 386+342 : 161+583 = 728 : 744 <br> | |||
Sample 6<br> | Sample 6<br> | ||
[[Image:SNP 6.png]]<br> | [[Image:SNP 6.png]]<br> | ||
{| {{table}} | |||
| align="center" style="background:#f0f0f0;"|'''Sample''' | |||
| align="center" style="background:#f0f0f0;"|'''peak location''' | |||
| align="center" style="background:#f0f0f0;"|'''base pair''' | |||
| align="center" style="background:#f0f0f0;"|'''base pair''' | |||
| align="center" style="background:#f0f0f0;"|'''peak value''' | |||
|- | |||
| ZL6-cust.ab1 ||150 ||T ||T ||746|| | |||
|- | |||
| ZL6-cust.ab1 ||149 ||T ||T ||588|| | |||
|- | |||
| ZL6-cust.ab1 ||150 ||T ||C ||199|| | |||
|- | |||
| ZL6-cust.ab1 ||151 ||C ||C ||1021|| | |||
|- | |||
| | |||
|} | |||
peak ratio: 746+588 : 199+1021 = 1334 : 1220 <br> | |||
Sample 7<br> | Sample 7<br> | ||
[[Image:SNP 7.png]]<br> | [[Image:SNP 7.png]]<br> | ||
{| {{table}} | |||
| align="center" style="background:#f0f0f0;"|'''Sample''' | |||
| align="center" style="background:#f0f0f0;"|'''peak location''' | |||
| align="center" style="background:#f0f0f0;"|'''base pair''' | |||
| align="center" style="background:#f0f0f0;"|'''base pair''' | |||
| align="center" style="background:#f0f0f0;"|'''peak value''' | |||
|- | |||
| ZL7-cust.ab1 ||197 ||A ||G ||234|| | |||
|- | |||
| ZL7-cust.ab1 ||196 ||G ||G ||476|| | |||
|- | |||
| ZL7-cust.ab1 ||197 ||A ||A ||1358|| | |||
|- | |||
| ZL7-cust.ab1 ||198 ||A ||A ||790|| | |||
|- | |||
| | |||
|} | |||
<br> | |||
peak ratio: 234+476 : 1358+790 = 710 : 2148 <br> | |||
The two samples we are really interested in are sample #6 and #7. The sample is GM20431 cDNA with rs 1264899 forward and reverse primer. The SNP location is rs 1264899. Then we will use software PeakPicker to compare and quantize the peaks.<br> | The two samples we are really interested in are sample #6 and #7. The sample is GM20431 cDNA with rs 1264899 forward and reverse primer. The SNP location is rs 1264899. Then we will use software PeakPicker to compare and quantize the peaks.<br> | ||
Here is the files of the original sequencing result files:<br> | Here is the files of the original sequencing result files:<br> | ||
* [https://genome-tech.ucsd.edu/LabNotes/index.php/Image:Sequencing_results.zip Sequencing results] | * [https://genome-tech.ucsd.edu/LabNotes/index.php/Image:Sequencing_results.zip Sequencing results] |
Revision as of 06:57, 1 January 2008
The sequencing results finally worked!
Sample | SNP | Sequencing result | |
1 | rs3753565 | yes | |
2 | rs2295680 | yes | |
3 | rs6103 | no | |
4 | rs1264899 | yes | |
5 | rs1264899 | yes | |
6 | rs1264899 | yes | |
7 | rs1264899 | yes | |
Sample 1
File:SNP 1.png
Sample | peak location | base pair | base pair | peak value | |
ZL1-cust.ab1 | 92 | N | C | 255 | |
ZL1-cust.ab1 | 94 | C | C | 695 | |
ZL1-cust.ab1 | 92 | N | T | 214 | |
ZL1-cust.ab1 | 93 | T | T | 613 | |
peak ratio: 255+695 : 214+613 = 950 : 827
Sample 2
File:SNP 2.png
Sample | peak location | base pair | base pair | peak value | |
ZL2-cust.ab1 | 96 | A | G | 190 | |
ZL2-cust.ab1 | 94 | G | G | 724 | |
ZL2-cust.ab1 | 96 | A | A | 209 | |
ZL2-cust.ab1 | 95 | A | A | 647 | |
peak ratio: 190+724 : 209+647 = 914 : 856
Sample 4
File:SNP 4.png
Sample | peak location | base pair | base pair | peak value | |
ZL4-cust.ab1 | 88 | C | C | 763 | |
ZL4-cust.ab1 | 89 | C | C | 731 | |
ZL4-cust.ab1 | 88 | C | T | 58 | |
ZL4-cust.ab1 | 87 | T | T | 475 | |
peak ratio: 763+731 : 58+475 = 1494 : 533
Sample 5
File:SNP 5.png
Sample | peak location | base pair | base pair | peak value | |
ZL5-cust.ab1 | 87 | T | T | 386 | |
ZL5-cust.ab1 | 86 | T | T | 342 | |
ZL5-cust.ab1 | 87 | T | C | 161 | |
ZL5-cust.ab1 | 88 | C | C | 583 | |
peak ratio: 386+342 : 161+583 = 728 : 744
Sample 6
File:SNP 6.png
Sample | peak location | base pair | base pair | peak value | |
ZL6-cust.ab1 | 150 | T | T | 746 | |
ZL6-cust.ab1 | 149 | T | T | 588 | |
ZL6-cust.ab1 | 150 | T | C | 199 | |
ZL6-cust.ab1 | 151 | C | C | 1021 | |
peak ratio: 746+588 : 199+1021 = 1334 : 1220
Sample 7
File:SNP 7.png
Sample | peak location | base pair | base pair | peak value | |
ZL7-cust.ab1 | 197 | A | G | 234 | |
ZL7-cust.ab1 | 196 | G | G | 476 | |
ZL7-cust.ab1 | 197 | A | A | 1358 | |
ZL7-cust.ab1 | 198 | A | A | 790 | |
peak ratio: 234+476 : 1358+790 = 710 : 2148
The two samples we are really interested in are sample #6 and #7. The sample is GM20431 cDNA with rs 1264899 forward and reverse primer. The SNP location is rs 1264899. Then we will use software PeakPicker to compare and quantize the peaks.
Here is the files of the original sequencing result files: