Daniel:Notebook/GenomeMiner/2013-9-17: Difference between revisions
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1. ''MockHL155_Master.m, Switch 2'' | 1. ''MockHL155_Master.m, Switch 2'' | ||
2. scp | 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 | 3. hl155bash.sh | ||
4. perl imp_count_mismatch.plx (Matt's error counting script) | 4. perl imp_count_mismatch.plx (Matt's error counting script) | ||
Line 24: | Line 24: | ||
So much poorer alignment than high substitutions, but still overall a high 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. |
Latest revision as of 00:05, 18 September 2013
Mock HL155 (Started 9/9/2013)[edit]
High Deletion Rate Test[edit]
Checking the results from the 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[edit]
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[edit]
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[edit]
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[edit]
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[edit]
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[edit]
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[edit]
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.