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==Verify Raw Probe Sequences== *We also wanted to verify the raw probe sequences that were sent to Custom Array for order between the two orders (original vs. filtered). Below are the raw files submitted to Custom Array for probe order: (both have multiple probes being ordered, so we need to filter to the correct primer version) Original 20140922 Probes: [[File:90k_oligos_30Sept2014.txt.gz]] Filtered Probes: [[File:CJWEI_May2015_12k.txt]] *We then want to remove the linker sequences and adapter sequences (AP1/AP2) as listed in the corresponding perl scripts and only extract the two capture arms for either hemo or phusion filtered probe sets. This was done in genemapster at </media/3TB_slot2/cjwei/Fate_Mapping/pp_design/ppDesigner_20140922/regular_probes_noC/filtered_Probes_20150523/verify_probes> *Based on the results, we see all but one probe for each hemo and phusion filtered probe sets contained within the original probe set. These are contained within the <comm.uniq_new.output> files for each: Unique to Filtered Probes (Hemo): CCAAATGTATCACGCCCAAAGC AGTGGTGATTCAACTGATTCTGATCGGATACGCATGAGGCT Unique to Filtered Probes (Phusion): TGTCCAGAGGTAGGCTAGGC ACCACTGTTTAGAGACACAGAC *Also, you'll notice that there are actually 1981 probes designed for each. This is because the "wc -l" linux command does not count the last line, which does not have a return key at the end of it *Based on this result, it looks like all the probes were ordered correctly except of the one extraneous probe ordered for each set
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