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=Mock HL155 ([[Daniel:Notebook/GenomeMiner/2013-9-9|Started 9/9/2013]])= [[Daniel:Notebook/GenomeMiner|Back to Calendar]] ==Full Reference Sequence Reads== From [[Daniel:Notebook/GenomeMiner/2013-9-20|Friday]], I'm still trying to generate reads that use the entire reference sequence to generate the mock reads (important when deletions are present). Also, the current code does not allow 2 errors per base (but allows up to n errors per read where n is the number of bases in the read). ===Workflow=== 1. MockHL155_Master.m, Switch 7 2. scp v4s1mockseq_extdel_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 Error Counts=== 1494539 substitutions (1.01 pct reads) 385509 insertions (0.26 pct reads) 74012 deletions (0.05 pct reads) ===Alignment Results=== 2959000 reads; of these: 2959000 (100.00%) were unpaired; of these: 105936 (3.58%) aligned 0 times 2842493 (96.06%) aligned exactly 1 time 10571 (0.36%) aligned >1 times 96.42% overall alignment rate ===Error Counting Results=== Error Rate: 1.128% Error Rate of Insertions: 0.189% Error Rate of Deletions: 0.029% Error Rate of Substitutions: 0.91%
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