AlanFung:LabNotes/2015/2015-7-14: Difference between revisions

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* 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.
* 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 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.
* 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.
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Revision as of 18:57, 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.
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