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

From ZhangLabWiki
Jump to navigation Jump to search
>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...")
 
>Alan6017518
Line 8: Line 8:
* 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