Daniel:Notebook/GenomeMiner/2013-9-16: Difference between revisions

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>Djacobse
>Djacobse
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[[Daniel:Notebook/GenomeMiner|Back to Calendar]]
[[Daniel:Notebook/GenomeMiner|Back to Calendar]]
==1% Substitutions==


Found the error in the MATLAB script that gave the strange results from [[Daniel:Notebook/GenomeMiner/2013-9-12#Analysis on Mimic Data|earlier]].  The script resused the same sequences for including error, meaning that the first few sequences had the right amount of error, but the error in each sequence compounded after each iteration.  So by the end the sequences were basically garbage.  The code has since been fixed.
Found the error in the MATLAB script that gave the strange results from [[Daniel:Notebook/GenomeMiner/2013-9-12#Analysis on Mimic Data|earlier]].  The script resused the same sequences for including error, meaning that the first few sequences had the right amount of error, but the error in each sequence compounded after each iteration.  So by the end the sequences were basically garbage.  The code has since been fixed.
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  Error Rate of Deletions: 2.08e-06%
  Error Rate of Deletions: 2.08e-06%
  Error Rate of Substitutions: 0.885%
  Error Rate of Substitutions: 0.885%
==Mimic Data==
Once again, this is based on the real data, with the numbers based on our previous calculations of error.
===Workflow===
1. ''MockHL155_Master.m, Switch 2''
2. scp v4s1_mockseq_1s.fq djacobse@132.239.135.41:/media/LTS_15T/DEJ_LTS/SeqStore/130628_HL155/mockseq/error1s/
3. hl155bash.sh
4. perl imp_count_mismatch.plx (Matt's error counting script)

Revision as of 00:36, 17 September 2013

Mock HL155 (Started 9/9/2013)

Back to Calendar

1% Substitutions

Found the error in the MATLAB script that gave the strange results from earlier. The script resused the same sequences for including error, meaning that the first few sequences had the right amount of error, but the error in each sequence compounded after each iteration. So by the end the sequences were basically garbage. The code has since been fixed.

Workflow

1. MockHL155_Master.m, Switch 2
2. scp v4s1_mockseq_1s.fq djacobse@132.239.135.41:/media/LTS_15T/DEJ_LTS/SeqStore/130628_HL155/mockseq/error1s/
3. hl155bash.sh
4. perl imp_count_mismatch.plx (Matt's error counting script)

MATLAB Substitution Counting Results

1. MockHL155_Master.m, Switch 4
Perfect Reads: 1790246 (60.5 pct)
Substitution Rate: 1479253 (1.0 pct)
Low Matches: 450 (0.0 pct)

Alignment Results

2959000 reads; of these:
 2959000 (100.00%) were unpaired; of these:
   64665 (2.19%) aligned 0 times
   2888951 (97.63%) aligned exactly 1 time
   5384 (0.18%) aligned >1 times
97.81% overall alignment rate

So this is much more promising than the results from last week with errors.

Error Counting Results

Error Rate: 0.885%
Error Rate of Insertions: 4.30e-05%
Error Rate of Deletions: 2.08e-06%
Error Rate of Substitutions: 0.885%

Mimic Data

Once again, this is based on the real data, with the numbers based on our previous calculations of error.

Workflow

1. MockHL155_Master.m, Switch 2
2. scp v4s1_mockseq_1s.fq djacobse@132.239.135.41:/media/LTS_15T/DEJ_LTS/SeqStore/130628_HL155/mockseq/error1s/
3. hl155bash.sh
4. perl imp_count_mismatch.plx (Matt's error counting script)