Daniel:Notebook/GenomeMiner/2013-9-18: Difference between revisions

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     5139 (0.17%) aligned >1 times
     5139 (0.17%) aligned >1 times
  95.52% overall alignment rate
  95.52% overall alignment rate
===Error Counting Results===
Error Rate: 0.0108202684905993
Error Rate of Insertions: 0.00194666217269491
Error Rate of Deletions: 5.48429204327288e-06
Error Rate of Substitutions: 0.00886812202586116

Revision as of 22:52, 18 September 2013

Mock HL155 (Started 9/9/2013)

Back to Calendar

Talked over with Matt today about the goals of the Mock HL155 project. The major goal is to test irregularities seen in the bowtie2 alignment data and check them using mock sequencing data, which we can control better. These irregularities include:

  • Specific sites where errors more frequently occur
  • General questions about bowtie's ability to accurately count the errors (is it off by a little bit?)
  • The dependence of bowtie alignment on the orientation of the reference strand (See 9/3/13)
  • The dependence of bowtie alignment on the length of the reference strand (See 9/3/13)

We've checked up, to an extent, on the site locations and the general questions about error count (although there are more tests I'd like to run). However, we should also check on the dependence of bowtie alignment on the reference strand length/orientation. To test this we will use four reference strands:

1. Original strand, full length (98 bp)
2. Reverse complement, full length (98 bp)
3. Original strand, read length (50 bp)
4. Reverse complement, read length (50 bp)

Additional testing (goal #2):

  • Use perfect base quality scores on mimic data

Mimic Data, Perfect Base Quality

Matt has discovered that the first and last bases of a read generally have higher error rates than the middle 40. To see if this is base-quality derived, I'm generating new reads with mimic style error (1.01% sub, 0.26% ins, 0.05% deletions)

Matlab Error Counts

628149 substitutions (0.42 pct) 
161459 insertions (0.11 pct) 
31202 deletions (0.02 pct)

Alignment Results

2959000 reads; of these:
 2959000 (100.00%) were unpaired; of these:
   11781 (0.40%) aligned 0 times
   2941663 (99.41%) aligned exactly 1 time
   5556 (0.19%) aligned >1 times
99.60% overall alignment rate

Error Counting Results

Error Rate: 0.526%
Error Rate of Insertions: 0.091%
Error Rate of Deletions: 1.82e-04%
Error Rate of Substitutions: 0.435%

Testing the Reference File

Alignment Results

Original Strand, Full (1)

Reverse Complement Strand, Full (2)

Original Strand, 50bp (3)

2959000 reads; of these:
 2959000 (100.00%) were unpaired; of these:
   132674 (4.48%) aligned 0 times
   2821187 (95.34%) aligned exactly 1 time
   5139 (0.17%) aligned >1 times
95.52% overall alignment rate


Error Counting Results

Error Rate: 0.0108202684905993 Error Rate of Insertions: 0.00194666217269491 Error Rate of Deletions: 5.48429204327288e-06 Error Rate of Substitutions: 0.00886812202586116