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