Daniel:Notebook/GenomeMiner/2013-8-14
HL155[edit]
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.
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[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