Daniel:Notebook/GenomeMiner/2013-9-18
Mock HL155 (Started 9/9/2013)
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)