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=Mock HL155 ([[Daniel:Notebook/GenomeMiner/2013-9-9|Started 9/9/2013]])= [[Daniel:Notebook/GenomeMiner|Back to Calendar]] ==High Deletion Rate Test== Checking the results from the [[Daniel:Notebook/GenomeMiner/2013-9-16|previous run]] by redoing the data, this time using a lower substitution rate and a higher deletion rate. Substitutions: 0.05%, Insertions: 0.26%, Deletions, 1.01%. ===Workflow=== 1. ''MockHL155_Master.m, Switch 2'' 2. scp v4s1_v4s1_mockseq_error_losubhidel.fq djacobse@132.239.135.41:/media/LTS_15T/DEJ_LTS/SeqStore/130628_HL155/mockseq/hidellowsub/ 3. hl155bash.sh 4. perl imp_count_mismatch.plx (Matt's error counting script) ===Alignment Results=== 2959000 reads; of these: 2959000 (100.00%) were unpaired; of these: 523061 (17.68%) aligned 0 times 2431720 (82.18%) aligned exactly 1 time 4219 (0.14%) aligned >1 times 82.32% overall alignment rate So much poorer alignment than high substitutions, but still overall a high rate. ===Error Counting Results=== Error Rate: 0.523% Error Rate of Insertions: 0.252% Error Rate of Deletions: 0.016% Error Rate of Substitutions: 0.255% ==Errors Bases 30 to 50== Rewrote part of the fastq error generating script to choose ranges of bases to have wrong. Can now insert errors wherever we please at any percentage we want. I selected the error to be the same percentages as the mimic data, but only from bases 30 to 50. ===Workflow=== 1. ''MockHL155_Master.m, Switch 5'' 2. scp djacobse@132.239.135.41:/media/LTS_15T/DEJ_LTS/SeqStore/130628_HL155/mockseq// 3. hl155bash.sh 4. perl imp_count_mismatch.plx (Matt's error counting script) '''MATLAB error counts''': 628508 substitutions (0.42 pct) 222963 insertions (0.15 pct) 42735 deletions (0.03 pct) The errors were meant to be mimic percent (1.01%s, 0.26%i, 0.05%d), but the actual percentages are lower, since the percentages given are probabilities, and automatcally bases 1:29 were without error. ===Alignment Results=== 2959000 reads; of these: 2959000 (100.00%) were unpaired; of these: 34339 (1.16%) aligned 0 times 2919032 (98.65%) aligned exactly 1 time 5629 (0.19%) aligned >1 times 98.84% overall alignment rate ===Error Counting Results=== Error Rate: 0.532% Error Rate of Insertions: 0.129% Error Rate of Deletions: 2.98e-04% Error Rate of Substitutions: 0.403% Looking at the basic error counting result, and comparing it to the MATLAB error counts before, the results are actually very close. Once again deletions has been undercounted by about 2 orders of magnitude, but substitutions and insertions are close, off by only about 0.02% each.
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