Daniel:Notebook/GenomeMiner/2013-9-23

From ZhangLabWiki
Revision as of 00:01, 24 September 2013 by >Djacobse (Created page with "=Mock HL155 (Started 9/9/2013)= Back to Calendar ==Full Reference Sequence Reads== From [[Daniel:No...")
(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to navigation Jump to search

Mock HL155 (Started 9/9/2013)

Back to Calendar

Full Reference Sequence Reads

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

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

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

Alignment Results

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

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