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===Change targetFile to contain strands w/o C=== *Each microsatellite target derived from the UCSC genome browser contains the microsatellite subunit sequence along with the number of times that subunit is repeated (ex: 10xAG). However, because we want to run bisulfite conversion prior to probe capture, we want to take into account that unmethylated C's will be converted to U's that would consequently be converted to T's after amplification. Consequently, we want to avoid the strand containing C's in the MS target and use the opposite strand. *To do this, we use the fact that the MS targets listed in the bed file refer to the Watson (+) strand of DNA in the reference. So, if there is a C in the MS target sequence (ex: 10xAC), we want to choose the Crick strand (-). If there is a G in the MS target sequence (ex: 10xAG), we want to choose the Watson strand (+). If there are neither C or G in the MS target, we can allow ppDesigner to choose the strand, and if there are both C and G in the MS target, we have to throw out the target altogether. *To accomplish this, I wrote a perl script <[[File:cw_2014-09-22_Microsat_filter_all.txt]]> that takes in the bed file containing all MS targets <[[File:cw_2014_09_22_Hg19_2nt-3nt-4nt_MS_location.txt]]> and outputs three targetFiles (one for each type of MS, i.e. 2nt, 3nt, 4nt) with the fourth column of the targetFile indicating the desired strand and the probe target subunit sequence changed to reflect that strand. If the script works, the probe target subunit sequences should not contain any C's (as the script changes the MS subunit sequence to reflect the corresponding strand). The command to run this is as follows: perl microsat_filter_all.pl hg19_2nt-3nt-4nt_MS_location.txt *The following are the resulting MS targetFiles that will be inputted into ppDesigner: [[File: cw_2014-09-22_targetFile_2nt.txt]] [[File: cw_2014-09-22_TargetFile_3nt.txt]] [[File: cw_2014-09-22_TargetFile_4nt.txt]]
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