34 lines
1.2 KiB
Plaintext
34 lines
1.2 KiB
Plaintext
1001 Ways to Make COP Better
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Simon Dear
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3 December 1991
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1. Incorporate quality considerations.
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Certain problems can slip through the detetion net. An example are
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overcalled bases in the consensus. Currently the whole raw data read
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is used, and overcalling will agree with the consensus. Overcalled
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runs of bases are very symptomatic of poor trace quality. If these
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could be detected and excluded from the coverage map, the problem
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would be detected.
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2. Running the program on contigs and regions of contigs.
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Cop could then be run on partially completed project databases.
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3. Provide explanations as to why a region is problematic.
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Maybe this isn't worth the effort to implement, but would be useful.
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4. Take into account strandedness.
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This would help detect regions where the coverage by good quality
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traces is poor.
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5. Interface to contig editor.
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The contig editor could center on and highlight regions where problems
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exist, speeding up the process.
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6. Consensus coverage.
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Currently if 10 good readings disagree with a region and just 1
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mediocre reading agrees, no problem is detected.
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7-1001. Make it detect 995 times as many problems.
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