AlanFung:LabNotes/2015/2015-7-14: Difference between revisions
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* I will pick the ones that have relatively low % trimmed (percentage of adapters being trimmed) and high % mapped rate from 2nd capture. | * I will pick the ones that have relatively low % trimmed (percentage of adapters being trimmed) and high % mapped rate from 2nd capture. | ||
* I will pick the ones with high % on target and low % clonal from 3rd capture. | * I will pick the ones with high % on target and low % clonal from 3rd capture. | ||
{| class="wikitable" class="wikitable" | {| class="wikitable" class="wikitable" class="wikitable" | ||
|- style="font-size:12pt" align="center" valign="bottom" | |- style="font-size:12pt" align="center" valign="bottom" | ||
| width=" | | width="61" height="15" | SAMPLE ID | ||
| width="94" | Total PE reads | | width="94" | Total PE reads | ||
| width="106" | Total reads | | width="106" | Total reads | ||
| width="136" | Total reads after trimming | | width="136" | Total reads after trimming | ||
| width=" | | width="158" | Total mapped reads | ||
| width="127" | %trimmed | | width="127" | %trimmed | ||
| width="100" | %mapped | | width="100" | %mapped | ||
Line 24: | Line 23: | ||
|- style="font-size:12pt" align="center" valign="bottom" | |- style="font-size:12pt" align="center" valign="bottom" | ||
| | | height="15" | 6T-2_map | ||
| align="center" | 7,489,616 | |||
| align="center" | | | align="center" | 14,979,232 | ||
| align="center" | | | align="center" | 14,638,550 | ||
| align="center" | | | align="center" | 12,820,323 | ||
| align="center" | | | align="center" | 2% | ||
| align="center" | | | align="center" | 88% | ||
| align="center" | | |||
| align="center" | | | align="center" | | ||
| align="center" | | | align="center" | | ||
Line 38: | Line 36: | ||
|- style="font-size:12pt" align="center" valign="bottom" | |- style="font-size:12pt" align="center" valign="bottom" | ||
| align="center" height="15" | | | align="center" height="15" | | ||
| align="center" | | | align="center" | | ||
| align="center" | | | align="center" | | ||
Line 50: | Line 47: | ||
|- style="font-size:12pt" align="center" valign="bottom" | |- style="font-size:12pt" align="center" valign="bottom" | ||
| height="15" | | height="15" | Sample | ||
| N_mapped_reads | | N_mapped_reads | ||
| N_non-clonal_reads | | N_non-clonal_reads | ||
Line 63: | Line 59: | ||
|- style="font-size:12pt" align="center" valign="bottom" | |- style="font-size:12pt" align="center" valign="bottom" | ||
| | | height="15" | 6P-3 | ||
| align="center" | 28,124,349 | |||
| align="center" | | | align="center" | 27,174,711 | ||
| align="center" | | | align="center" | 20,126,384 | ||
| align="center" | | | align="center" | 19,455,168 | ||
| align="center" | | | align="center" | 7,299,019 | ||
| align="center" | | | align="center" | 48,605 | ||
| align="center" | | | align="center" | 71.60% | ||
| align="center" | | | align="center" | 3.40% | ||
| align="center" | | |||
| align="center" | 254 | | align="center" | 254 | ||
|- style="font-size:12pt" align="center" valign="bottom" | |- style="font-size:12pt" align="center" valign="bottom" | ||
| | | height="15" | PCP-3 | ||
| align="center" | 9,225,527 | |||
| align="center" | | | align="center" | 9,067,481 | ||
| align="center" | | | align="center" | 6,226,370 | ||
| align="center" | | | align="center" | 6,133,490 | ||
| align="center" | | | align="center" | 1,984,048 | ||
| align="center" | | | align="center" | 47,803 | ||
| align="center" | | | align="center" | 67.50% | ||
| align="center" | | | align="center" | 1.70% | ||
| align="center" | | |||
| align="center" | 210 | | align="center" | 210 | ||
|- style="font-size:12pt" align="center" valign="bottom" | |- style="font-size:12pt" align="center" valign="bottom" | ||
| | | height="15" | NC-30 | ||
| align="center" | 15,359,075 | |||
| align="center" | | | align="center" | 13,957,906 | ||
| align="center" | | | align="center" | 9,350,399 | ||
| align="center" | | | align="center" | 8,223,219 | ||
| align="center" | | | align="center" | 3,641,546 | ||
| align="center" | | | align="center" | 45,664 | ||
| align="center" | | | align="center" | 60.90% | ||
| align="center" | | | align="center" | 9.10% | ||
| align="center" | | |||
| align="center" | 157 | | align="center" | 157 | ||
|} | |} |
Revision as of 18:59, 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.
- I am going to pick 1x tumor 2x plasma sample and 1x NC plasma
- I will pick the ones that have relatively low % trimmed (percentage of adapters being trimmed) and high % mapped rate from 2nd capture.
- I will pick the ones with high % on target and low % clonal from 3rd capture.
SAMPLE ID | Total PE reads | Total reads | Total reads after trimming | Total mapped reads | %trimmed | %mapped | |||
6T-2_map | 7,489,616 | 14,979,232 | 14,638,550 | 12,820,323 | 2% | 88% | |||
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 |
6P-3 | 28,124,349 | 27,174,711 | 20,126,384 | 19,455,168 | 7,299,019 | 48,605 | 71.60% | 3.40% | 254 |
PCP-3 | 9,225,527 | 9,067,481 | 6,226,370 | 6,133,490 | 1,984,048 | 47,803 | 67.50% | 1.70% | 210 |
NC-30 | 15,359,075 | 13,957,906 | 9,350,399 | 8,223,219 | 3,641,546 | 45,664 | 60.90% | 9.10% | 157 |