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

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


===Results===
===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 reads; of these:
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So this is much more promising than the results from last week with errors.
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. Actual percentages: 1.01% substitutions, 0.26% insertions, 0.05% deletions
===Workflow===
1. ''MockHL155_Master.m, Switch 2''
2. scp v4s1_mockseq_error_mimic.fq djacobse@132.239.135.41:/media/LTS_15T/DEJ_LTS/SeqStore/130628_HL155/mockseq/mimicerror/
3. hl155bash.sh
4. perl imp_count_mismatch.plx (Matt's error counting script)
===Alignment Results===
2959000 reads; of these:
  2959000 (100.00%) were unpaired; of these:
    133942 (4.53%) aligned 0 times
    2819919 (95.30%) aligned exactly 1 time
    5139 (0.17%) aligned >1 times
95.47% overall alignment rate
===Error Count Results===
Error Rate: 1.08%
Error Rate of Insertions: 0.195%
Error Rate of Deletions: 5.52e-04%
Error Rate of Substitutions: 0.887%

Latest revision as of 00:53, 17 September 2013

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

Back to Calendar

1% Substitutions[edit]

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[edit]

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[edit]

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[edit]

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[edit]

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[edit]

Once again, this is based on the real data, with the numbers based on our previous calculations of error. Actual percentages: 1.01% substitutions, 0.26% insertions, 0.05% deletions

Workflow[edit]

1. MockHL155_Master.m, Switch 2
2. scp v4s1_mockseq_error_mimic.fq djacobse@132.239.135.41:/media/LTS_15T/DEJ_LTS/SeqStore/130628_HL155/mockseq/mimicerror/
3. hl155bash.sh
4. perl imp_count_mismatch.plx (Matt's error counting script)

Alignment Results[edit]

2959000 reads; of these:
 2959000 (100.00%) were unpaired; of these:
   133942 (4.53%) aligned 0 times
   2819919 (95.30%) aligned exactly 1 time
   5139 (0.17%) aligned >1 times
95.47% overall alignment rate

Error Count Results[edit]

Error Rate: 1.08%
Error Rate of Insertions: 0.195%
Error Rate of Deletions: 5.52e-04%
Error Rate of Substitutions: 0.887%