Daniel:Notebook/GenomeMiner/2013-9-19: Difference between revisions

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>Djacobse
(Created page with "=Mock HL155 (Started 9/9/2013)= Back to Calendar ==Single Error per Read== Goal of this test is to ...")
 
>Djacobse
Line 14: Line 14:
  4. perl imp_count_mismatch.plx (Matt's error counting script)
  4. perl imp_count_mismatch.plx (Matt's error counting script)


'''MATLAB Error Count''':
1493243 substitutions (1.01 pct reads)
386123 insertions (0.26 pct reads)
73712 deletions (0.05 pct reads)


1493243 substitutions (1.01 pct reads)
===Alignment Results===
386123 insertions (0.26 pct reads)
73712 deletions (0.05 pct reads)

Revision as of 18:39, 19 September 2013

Mock HL155 (Started 9/9/2013)

Back to Calendar

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:

1493243 substitutions (1.01 pct reads) 
386123 insertions (0.26 pct reads) 
73712 deletions (0.05 pct reads)

Alignment Results