Daniel:Notebook/GenomeMiner/2013-9-18
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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)