Daniel:Notebook/GenomeMiner/2013-9-23

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Mock HL155 (Started 9/9/2013)[edit]

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Full Reference Sequence Reads[edit]

From Friday, I'm still trying to generate reads that use the entire reference sequence to generate the mock reads (important when deletions are present). Also, the current code does not allow 2 errors per base (but allows up to n errors per read where n is the number of bases in the read).

Workflow[edit]

1. MockHL155_Master.m, Switch 7
2. scp v4s1mockseq_extdel_errormimic.fq djacobse@132.239.135.41:/media/LTS_15T/DEJ_LTS/SeqStore/130628_HL155/mockseq/extdeletions/
3. hl155bash.sh
4. perl imp_count_mismatch.plx

MATLAB Error Counts[edit]

1494539 substitutions (1.01 pct reads) 
385509 insertions (0.26 pct reads) 
74012 deletions (0.05 pct reads) 

Alignment Results[edit]

2959000 reads; of these:
 2959000 (100.00%) were unpaired; of these:
   105936 (3.58%) aligned 0 times
   2842493 (96.06%) aligned exactly 1 time
   10571 (0.36%) aligned >1 times
96.42% overall alignment rate

Error Counting Results[edit]

Error Rate: 1.128%
Error Rate of Insertions: 0.189%
Error Rate of Deletions: 0.029%
Error Rate of Substitutions: 0.91%