Daniel:Notebook/GenomeMiner/2013-9-17

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Mock HL155 (Started 9/9/2013)[edit]

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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.