Daniel:Notebook/GenomeMiner/2013-9-20: Difference between revisions

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===Alignment Results===
===Alignment Results===
2959000 reads; of these:
  2959000 (100.00%) were unpaired; of these:
    7858 (0.27%) aligned 0 times
    2945510 (99.54%) aligned exactly 1 time
    5632 (0.19%) aligned >1 times
99.73% overall alignment rate

Revision as of 20:37, 20 September 2013

Mock HL155 (Started 9/9/2013)

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Mimic Data, Bases 30 to 50

Last mimic data bases 30 to 50 actually put insertions/deletions from bases 1 to 29, not 30 to 50, so for good measure I'm repeating the code using the correct 30 to 50 range. This will make it directly comparable to the perfect base quality mimic data from 9/18.

Workflow

1. MockHL155_Master.m, Switch 5
2. scp v4s1mockseq_errormimic_30to50bp.fq djacobse@132.239.135.41:/media/LTS_15T/DEJ_LTS/SeqStore/130628_HL155/mockseq/errormimic_30to50/
3. ./hl155bash.sh
4. perl imp_count_mismatch.plx

Matlab Error Counts

627618 substitutions (0.42 pct) 
161680 insertions (0.11 pct) 
30992 deletions (0.02 pct) 

Alignment Results

2959000 reads; of these:
 2959000 (100.00%) were unpaired; of these:
   7858 (0.27%) aligned 0 times
   2945510 (99.54%) aligned exactly 1 time
   5632 (0.19%) aligned >1 times
99.73% overall alignment rate