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==Full Reference Sequence== Just like [[Daniel:Notebook/GenomeMiner/2013-9-19|yesterday]], I'm using the real bases for deletions, instead of random bases at the end. This newest code should also be the fastest code yet, and boasts one more potentially important change. All other iterations (except the single error per read) would roll for errors in every base, including those that already had errors. The new code only gives potentially one error per base, meaning a base that has a substitution will not also be deleted (and other such errors). ===Workflow=== 1. MockHL155_Master.m, Switch 7 2. scp v4s1mockseq_extseq_errormimic.fq djacobse@132.239.135.41:/media/LTS_15T/DEJ_LTS/SeqStore/130628_HL155/mockseq/extdeletions/ 3. ./hl155bash.sh 4. perl imp_count_mismatch.plx ===MATLAB Results=== 1493592 substitutions (0.52 pct reads) 384892 insertions (0.13 pct reads) 73602 deletions (0.03 pct reads) ===Alignment Results=== 2959000 reads; of these: 2959000 (100.00%) were unpaired; of these: 688259 (23.26%) aligned 0 times 2266933 (76.61%) aligned exactly 1 time 3808 (0.13%) aligned >1 times 76.74% overall alignment rate ===Error Counting Results=== Error Rate: 4.301% Error Rate of Insertions: 2.79% Error Rate of Deletions: 0 % Error Rate of Substitutions: 1.51% These results seem really weird. I'm going to have to look over the Switch 7 code again.
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