Alice:LabNotes/2007-12-5: Difference between revisions
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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 = 1.051 : 1 <br><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 = 0.811 : 1 <br><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 = 8.557 : 1 <br><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 = 4.091 : 1 <br><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 = 6.503 : 1 <br><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 = 0.286 : 1 <br><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 | Here is the files of the original sequencing result files:<br> | ||
* [https://genome-tech.ucsd.edu/LabNotes/index.php/ | * [https://genome-tech.ucsd.edu/LabNotes/index.php/Image:Sequencing_results.zip Sequencing results] | ||
Latest revision as of 20:55, 31 March 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 = 1.051 : 1
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 = 0.811 : 1
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 = 8.557 : 1
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 = 4.091 : 1
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 = 6.503 : 1
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 = 0.286 : 1
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: