Daniel:Notebook/GenomeMiner/2013-8-14: Difference between revisions
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[[Image:V6_zeros.png|400px]]|[[Image:V4_zeros.png|400px]] | [[Image:V6_zeros.png|400px]]|[[Image:V4_zeros.png|400px]] | ||
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==Error Counting== | |||
Using Matt's revamped script we were able to count the errors/mismatches on a per base scale. Again, I had to modify the script to run it with my probe labeling method. | |||
Error Rate: 0.0208727984165367 = 2.08727984165367% | |||
Error Rate of Insertions: 0.00110582525321098 = 0.110582525321098% | |||
Error Rate of Deletions: 0.0118930582786553 = 1.18930582786553% | |||
Error Rate of Substitutions: 0.00787391488467041 = 0.787391488467041% |
Revision as of 19:46, 14 August 2013
HL155
[[Daniel:Notebook/GenomeMiner|
Redid some statistics on probe counts. These will also be in the lab meeting for today, but I will include them here as well.
Probe Count histograms
Just the same as previously reported, but with smaller bins. Normalization for x axis is also changed. Now it is based on the expected number of reads, calculated by dividing the total number of reads for a given set by the total number of probes in that set (usually around 250 reads). So a one means the probes were amplified more or less linearly, <1 means they were underamplified, and >1 means the probe was overamplifed.
Pie Chart Statistics
Pie chart showing probe count statistics. Probe counts are divided into 3 classes: 0 reads, over-amplified (described as >5x the expected count), and normally amplified reads.
File:V6 zeros.png|File:V4 zeros.pngError Counting
Using Matt's revamped script we were able to count the errors/mismatches on a per base scale. Again, I had to modify the script to run it with my probe labeling method.
Error Rate: 0.0208727984165367 = 2.08727984165367% Error Rate of Insertions: 0.00110582525321098 = 0.110582525321098% Error Rate of Deletions: 0.0118930582786553 = 1.18930582786553% Error Rate of Substitutions: 0.00787391488467041 = 0.787391488467041%