Daniel:Notebook/GenomeMiner/2013-9-16

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Revision as of 22:01, 16 September 2013 by >Djacobse (→‎Mock HL155 (Started 9/9/2013))
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Mock HL155 (Started 9/9/2013)

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Found the error in the MATLAB script that gave the strange results from earlier. The script resused the same sequences for including error, meaning that the first few sequences had the right amount of error, but the error in each sequence compounded after each iteration. So by the end the sequences were basically garbage. The code has since been fixed.

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:
   64665 (2.19%) aligned 0 times
   2888951 (97.63%) aligned exactly 1 time
   5384 (0.18%) aligned >1 times
97.81% overall alignment rate

So this is much more promising than the results from last week with errors.

Error Counting Results

Error Rate: 0.885% Error Rate of Insertions: 4.30e-05% Error Rate of Deletions: 2.08e-06% Error Rate of Substitutions: 0.885%