AlanFung:LabNotes/ASE/2010/2010-9-13
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Analysis of the Hues6/BJ hybrid data
Summary of experiments
Index Table
- 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
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 HL071 run (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.