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==Verify Scripts== *Below are the scripts used when Dr. Zhang finalized the filtered probe sets for order at Custom Array: [[File:cw_20150702_Probe2padlock13May2014V4.txt]] 20150523 New Probes (new set of 8000 not used in this analysis, v4) [[File:cw_20150702_Probe2padlock13May2014V6.txt]] Filtered Hemo Probes (v6) [[File:cw_20150702_Probe2padlock13May2014V8.txt]] Filtered Phusion Probes (v8) *Below is the script used to make the original probe order from 20140922: [[File:Probe2padlock30Sept2014V6.txt]] *There are a few differences between the new probes from teh old probes based on the scripts (v6 and v8 vs. the original probe script) **LinkerL is 4nt longer (with TATT added to 3' end) for the new probes **LinkerR is 8nt longer (with CAGGCAGA added to 5' end) **The UMI sequence is 6nt vs the original 8nt used in the original probe **For the new probes, the maxH1H2Len parameter is 4nt longer than the original (maxH1H2Len=46). Because the original ppDesigner parameter of H1_plut_H2_Len was original set to 42nt for the original 20140922 probes along with the new filtered probes (which was just a copy and paste of lines from the original probe file), there is a 4nt poly-T filler within every new padlock probe designed *Based on these differences, it doesn't look like there is anything that would cause drastically worse capture
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