Daniel:Notebook/GenomeMiner/2013-9-19

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Revision as of 19:49, 19 September 2013 by >Djacobse (→‎Alignment Results)
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Mock HL155 (Started 9/9/2013)

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Single Error per Read

Goal of this test is to see if bowtie's alignment results are dependent on the number of errors per read. So far the errors have been completely random, with each base potentially getting a substitution, insertion, or deletion, or even several errors. This new iteration rolls to see if an error will occur at all, and based on its roll also determines which of the three error types it will give.

Workflow

1. MockHL155_Master.m, Switch 6
2. scp v4s1mockseq_1errperread_mimic.fq djacobse@132.239.135.41:/media/LTS_15T/DEJ_LTS/SeqStore/130628_HL155/mockseq/error1per/
3. hl155bash.sh
4. perl imp_count_mismatch.plx (Matt's error counting script)

MATLAB Error Count:

1494000 substitutions (1.01 pct) 
384556 insertions (0.26 pct) 
73592 deletions (0.05 pct) 

Alignment Results

2959000 reads; of these:
 2959000 (100.00%) were unpaired; of these:
   25319 (0.86%) aligned 0 times
   2928519 (98.97%) aligned exactly 1 time
   5162 (0.17%) aligned >1 times
99.14% overall alignment rate

Error Counting Results

Error Rate: 1.298%
Error Rate of Insertions: 0.241%
Error Rate of Deletions: 2.45e-04%
Error Rate of Substitutions: 1.057%