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===Merge to determine intersection of BSPP and regular probes=== *This step is done in the folder in genemapster at </media/3TB_slot2/cjwei/Fate_Mapping/pp_design/ppDesigner_20140922/intersection_BSPP-regular_probes_noC> *The protocol for this step is short and only requires as input the concatenated files of each type of probe (Bisulfite and Regular), i.e. there will be two files [[File:Hg19_BSPP_probes_noC_20140922.txt]] and [[File:Hg19_regular_probes_noC_20140922.txt]] 1) We first sort each of these two input files based on targetID using the following commands (to make processing go by quicker): sort -k2 hg19_BSPP_probes_noC_20140922.txt >hg19_BSPP_probes_noC_20140922.txt.sorted sort -k2 hg19_regular_probes_noC_20140922.txt >hg19_regular_probes_noC_20140922.txt.sorted 2) We then obtain only the targetID's from each file by using the cut linux command cut -f2 hg19_BSPP_probes_noC_20140922.txt >hg19_BSPP_probes_noC_20140922.cut cut -f2 hg19_regular_probes_noC_20140922.txt >hg19_regular_probes_noC_20140922.cut 3) Next, I found the intersection between the two targetID *.cut files using grep grep -Fx -f hg19_BSPP_probes_noC_20140922.cut hg19_regular_probes_noC_20140922.cut | sort - >intersection.cut 4) Finally, I used the previous merge_probe_files.pl script to obtain only probes that target those specific targetID's perl merge_probe_files.pl intersection.cut hg19_BSPP_probes_noC_20140922.txt.sorted hg19_BSPP_probes_noC_20140922.intersected.txt perl merge_probe_files.pl intersection.cut hg19_regular_probes_noC_20140922.txt.sorted hg19_regular_probes_noC_20140922.intersected.txt *The output files can be used if we want a probe set that is directly comparable between bisulfite converted DNA and non-treated DNA, to determine if capture efficiency is different between one or the other.
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