Daniel:Notebook/GenomeMiner/2013-8-14

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HL155[edit]

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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[edit]

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.

File:Probecounts-labeled.png

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.png

Error Counting[edit]

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%

Comparison with Custom Array/Agilent Probes

File:ProbeComparison Improved.png