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="64" height="15" | Experiment
| width="61" height="15" | SAMPLE ID
| width="61" | 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="213" | Total mapped reads
| 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"
| align="center" height="15" | 2
| height="15" | 6T-2_map
| 6T-2_map
| align="center" | 7,489,616
| align="center" | 7489616
| align="center" | 14,979,232
| align="center" | 14979232
| align="center" | 14,638,550
| align="center" | 14638550
| align="center" | 12,820,323
| align="center" | 12820323
| align="center" | 2%
| align="center" | 0.02
| align="center" | 88%
| align="center" | 0.88
| 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" |  
| align="center" |  
Line 50: Line 47:


|- style="font-size:12pt" align="center" valign="bottom"
|- style="font-size:12pt" align="center" valign="bottom"
| height="15" | Experiment
| height="15" | Sample
| 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"
| align="center" height="15" | 3
| height="15" | 6P-3
| 6P-3
| align="center" | 28,124,349
| align="center" | 28124349
| align="center" | 27,174,711
| align="center" | 27174711
| align="center" | 20,126,384
| align="center" | 20126384
| align="center" | 19,455,168
| align="center" | 19455168
| align="center" | 7,299,019
| align="center" | 7299019
| align="center" | 48,605
| align="center" | 48605
| align="center" | 71.60%
| align="center" | 0.716
| align="center" | 3.40%
| align="center" | 0.034
| align="center" | 254
| align="center" | 254


|- style="font-size:12pt" align="center" valign="bottom"
|- style="font-size:12pt" align="center" valign="bottom"
| align="center" height="15" | 3
| height="15" | PCP-3
| PCP-3
| align="center" | 9,225,527
| align="center" | 9225527
| align="center" | 9,067,481
| align="center" | 9067481
| align="center" | 6,226,370
| align="center" | 6226370
| align="center" | 6,133,490
| align="center" | 6133490
| align="center" | 1,984,048
| align="center" | 1984048
| align="center" | 47,803
| align="center" | 47803
| align="center" | 67.50%
| align="center" | 0.675
| align="center" | 1.70%
| align="center" | 0.017
| align="center" | 210
| align="center" | 210


|- style="font-size:12pt" align="center" valign="bottom"
|- style="font-size:12pt" align="center" valign="bottom"
| align="center" height="15" | 3
| height="15" | NC-30
| NC-30
| align="center" | 15,359,075
| align="center" | 15359075
| align="center" | 13,957,906
| align="center" | 13957906
| align="center" | 9,350,399
| align="center" | 9350399
| align="center" | 8,223,219
| align="center" | 8223219
| align="center" | 3,641,546
| align="center" | 3641546
| align="center" | 45,664
| align="center" | 45664
| align="center" | 60.90%
| align="center" | 0.609
| align="center" | 9.10%
| align="center" | 0.091
| 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