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===Workflow=== 1) Convert using BCL converter 2)Demultiplex [[Media:Demultiplex.txt|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 [[Media:mkdir.txt|make directory script]] [[Media:merge_68_71.txt|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 [[Media:density_plot.txt|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 [[Media:baseCalls2Ase2_B5.pl|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]]
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