AlanFung:LabNotes/ASE/2010/2010-9-13

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Analysis of the Hues6/BJ hybrid data[edit]

Summary of experiments[edit]

Index Table[edit]

  • tmp=HL071
  • tmp2=HL068_2
gDNA cDNA
HL068_2 HL071 HL068_2 HL071
5+6 5 + 6 7+8 7+8
IND1 N/A H1 gDNA IND1 1000s 1000s
IND2 1000ips 1000ips IND2 1000ips 1000ips
IND3 1034ips 1034ips IND3 1034ips 1034ips
IND4 A2 A2 IND4 A2 A2
IND5 B4 B4 IND5 B4 B4
IND6 1016ips 1016ips IND6 1016s 1016s
IND7 N/A N/A IND7 1016ips 1016ips
IND8 B5 B5 IND8 B5ips B5ips
IND9 Hues6 Hues6 IND9 Hues6 Hues6
IND10 N/A N/A IND10 BJ BJ
IND11 BJ BJ IND11 N/A 1034s
IND12 N/A H1 cDNA IND12 N/A N/A
Wiki KZ 7_22 HL 8_26 HL 7_26 HL 8_26

Workflow[edit]

1) Convert using BCL converter
2)Demultiplex
Script for demultiplex
3)Combine files
Use Excel to create script for merging ID filles from serval lanes of Data to one file
Create separate files for all samples
make directory script
Merge 68 and 71 script
4)Run aseBowtieSam.pl
5)Run baseCalls2Ase.pl on local machine
*Dr. Zhang finds out the two libraries 1034iPS_CDNA and A2_CDNA are mixed up from the similarity plot
*I double check the script for merging the files and don't see any problem
*nothing changed for the library, when making the new library for HL071run(new library was mixture of 1034s_CDNA and HL068 cDNA library) 
*Will go ahead and make a change to the files by reemerging the files.

6)Plot graph on the expect allele ratio 
R script
File:1000iPSg 1034iPSg B4 Fratios Hist.jpg
File:1000iPSg 1034iPSg B4 Fratios Desity.jpg
*Close to the expected ratio of 2/3
Repeat same procedure to generate data for B5 hybrid
File:1016iPSg 1034iPSg B5g B5c hist.jpg
File:1016iPSg 1034iPSg B5g B5c density.jpg
Used new script for B5 from Dr. Zhang
script
File:1016iPSg B5g B5c hist.jpg
File:1016iPSg B5g B5c density.jpg
File:1016iPSg B5g B5c norm hist.jpg
File:1016iPSg B5g B5c norm density.jpg