AlanFung:LabNotes/2015/2015-7-14: Difference between revisions
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>Alan6017518 (Created page with "==Swift vs. Kapa== * We are interested in the performance of the Swift Bioscience Methyl-Seq DNa library kit * Since we have WGB libraries made using Kapa we can compare swif...") |
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* After discussing with Dinh I am going to pick 1x tumor 1x plasma sample and 2x NC plasma | * After discussing with Dinh I am going to pick 1x tumor 1x plasma sample and 2x NC plasma | ||
* I will pick the ones that have relatively low % trimmed (percentage of adapters being trimmed) and high % mapped rate. | * I will pick the ones that have relatively low % trimmed (percentage of adapters being trimmed) and high % mapped rate. | ||
{| class="wikitable" class="wikitable" | |||
|- style="font-size:12pt" align="center" valign="bottom" | |||
| width="64" height="15" | Experiment | |||
| width="61" | SAMPLE ID | |||
| width="94" | Total PE reads | |||
| width="106" | Total reads | |||
| width="136" | Total reads after trimming | |||
| width="213" | Total mapped reads | |||
| width="127" | %trimmed | |||
| width="100" | %mapped | |||
| align="center" width="75" | | |||
| align="center" width="58" | | |||
| align="center" width="99" | | |||
|- style="font-size:12pt" align="center" valign="bottom" | |||
| align="center" height="15" | 2 | |||
| 6T-2_map | |||
| align="center" | 7489616 | |||
| align="center" | 14979232 | |||
| align="center" | 14638550 | |||
| align="center" | 12820323 | |||
| align="center" | 0.02 | |||
| align="center" | 0.88 | |||
| align="center" | | |||
| align="center" | | |||
| align="center" | | |||
|- style="font-size:12pt" align="center" valign="bottom" | |||
| align="center" height="15" | | |||
| align="center" | | |||
| align="center" | | |||
| align="center" | | |||
| align="center" | | |||
| align="center" | | |||
| align="center" | | |||
| align="center" | | |||
| align="center" | | |||
| align="center" | | |||
| align="center" | | |||
|- style="font-size:12pt" align="center" valign="bottom" | |||
| height="15" | Experiment | |||
| Sample | |||
| N_mapped_reads | |||
| N_non-clonal_reads | |||
| N_on-target_reads | |||
| N_non-clonal_on-target_reads | |||
| N_on-target_haplotypes | |||
| N_target_coverred | |||
| Pct_on-target | |||
| Pct_clonal | |||
| Enrichment_factor | |||
|- style="font-size:12pt" align="center" valign="bottom" | |||
| align="center" height="15" | 3 | |||
| 6P-3 | |||
| align="center" | 28124349 | |||
| align="center" | 27174711 | |||
| align="center" | 20126384 | |||
| align="center" | 19455168 | |||
| align="center" | 7299019 | |||
| align="center" | 48605 | |||
| align="center" | 0.716 | |||
| align="center" | 0.034 | |||
| align="center" | 254 | |||
|- style="font-size:12pt" align="center" valign="bottom" | |||
| align="center" height="15" | 3 | |||
| PCP-3 | |||
| align="center" | 9225527 | |||
| align="center" | 9067481 | |||
| align="center" | 6226370 | |||
| align="center" | 6133490 | |||
| align="center" | 1984048 | |||
| align="center" | 47803 | |||
| align="center" | 0.675 | |||
| align="center" | 0.017 | |||
| align="center" | 210 | |||
|- style="font-size:12pt" align="center" valign="bottom" | |||
| align="center" height="15" | 3 | |||
| NC-30 | |||
| align="center" | 15359075 | |||
| align="center" | 13957906 | |||
| align="center" | 9350399 | |||
| align="center" | 8223219 | |||
| align="center" | 3641546 | |||
| align="center" | 45664 | |||
| align="center" | 0.609 | |||
| align="center" | 0.091 | |||
| align="center" | 157 | |||
|} |
Revision as of 18:55, 14 July 2015
Swift vs. Kapa
- We are interested in the performance of the Swift Bioscience Methyl-Seq DNa library kit
- Since we have WGB libraries made using Kapa we can compare swift against it.
- Experiment was done
- Data analysis was done by Dr. Zhang
Samples
- We only have 12 reactions from the swift methyl-seq kit and Dana needs to use it for her project so I can work on 4 samples.
- After discussing with Dinh I am going to pick 1x tumor 1x plasma sample and 2x NC plasma
- I will pick the ones that have relatively low % trimmed (percentage of adapters being trimmed) and high % mapped rate.
Experiment | SAMPLE ID | Total PE reads | Total reads | Total reads after trimming | Total mapped reads | %trimmed | %mapped | |||
2 | 6T-2_map | 7489616 | 14979232 | 14638550 | 12820323 | 0.02 | 0.88 | |||
Experiment | Sample | N_mapped_reads | N_non-clonal_reads | N_on-target_reads | N_non-clonal_on-target_reads | N_on-target_haplotypes | N_target_coverred | Pct_on-target | Pct_clonal | Enrichment_factor |
3 | 6P-3 | 28124349 | 27174711 | 20126384 | 19455168 | 7299019 | 48605 | 0.716 | 0.034 | 254 |
3 | PCP-3 | 9225527 | 9067481 | 6226370 | 6133490 | 1984048 | 47803 | 0.675 | 0.017 | 210 |
3 | NC-30 | 15359075 | 13957906 | 9350399 | 8223219 | 3641546 | 45664 | 0.609 | 0.091 | 157 |