AlanFung:LabNotes/2015/2015-7-14
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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.
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 |