Daniel:Notebook/GenomeMiner/2013-9-17

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Revision as of 20:28, 17 September 2013 by >Djacobse (→‎Workflow)
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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_mockseq_1s.fq djacobse@132.239.135.41:/media/LTS_15T/DEJ_LTS/SeqStore/130628_HL155/mockseq/error1s/
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.