Daniel:Notebook/GenomeMiner/2013-9-17

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Revision as of 21:39, 17 September 2013 by >Djacobse (→‎Errors Bases 30 to 50)
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Mock HL155 (Started 9/9/2013)

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High Deletion Rate Test

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

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 as the mimic data.

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)