Daniel:Notebook/GenomeMiner/2013-8-13

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HL155[edit]

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Continuing Matt's pipeline. Looking over the perl script.

I believe I fixed the perl script (uses my notation): File:Count mismatch.txt

Results[edit]

Error Rate: 2.08727984165367

  Total reads Filtered reads Perfect match 1 ins/del 1 sub 2 ins/del 2 sub 1 ins/del & 1 sub 3+
Number 20727275 15082383 4411040 3584377 2417322 1893421 754110 1647242 374871
Percent 100 72.77 21.28 17.29 11.66 9.13 3.64 7.95 1.81

Comparing this against Matt's results, it looks like the MYcroarray probes have more errors. Around 75% of Matt's reads were perfect, but mine tend to have at least 1 error (only around 20% perfect).

Also analyzed the results (partly). See here for analysis.