Daniel:Notebook/GenomeMiner
Link to useful Perl website: Basic Perl
Calendar[edit]
<calendar> name=Daniel:Notebook/GenomeMiner format=%name/%year-%month-%day date=2013/02/01 view=oneyear </calendar>
Useful Linux Commands[edit]
SCP to laptop
%% scp <remote user>@<remote machine>:<remote path> <local file> scp djacobse@132.239.135.41:/home/djacobse/HL155/130628_HL155/probecount.csv probecount.csv
Chmod of Bash Script
chmod u+x <bashscriptname>
HL155[edit]
Analysis of 3 probe production companies: MYcroarray, Agilent, and Custom Array.
Data Analysis Spreadsheet: File:ProbeComparison.xlsx
MATLAB Master File: File:HL155 Master.txt
Raw Data[edit]
Probe Set | Total reads | Filtered reads | Perfect match | 1 ins/del | 1 sub | 2 ins/del | 2 sub | 1 ins/del & 1 sub | 3+ |
Mycroarray | 20727275 | 15082383 | 4411040 | 3584377 | 2417322 | 1893421 | 754110 | 1647242 | 374871 |
Agilent 0 gap | 4953642 | 4448339 | 3294962 | 102309 | 808922 | 12240 | 129671 | 24455 | 75780 |
Agilent 20 gap | 4052727 | 3578431 | 2676974 | 101104 | 619290 | 14445 | 92296 | 20184 | 54138 |
Agilent | 9006369 | 8026770 | 5971936 | 203413 | 1428212 | 26685 | 221967 | 44639 | 129918 |
Custom Array 12K | 5195976 | 4533981 | 3176472 | 77874 | 962022 | 4934 | 178599 | 30019 | 104061 |
As Percent
Probe Set | Total reads | Filtered reads (%) | Perfect match (%Filtered) | 1 ins/del (%Filtered) | 1 sub (%Filtered) | 2 ins/del (%Filtered) | 2 sub (%Filtered) | 1 ins/del & 1 sub (%Filtered) | 3+ (%Filtered) |
Mycroarray | 20727275 | 72.8 | 29.2 | 23.8 | 16.0 | 12.6 | 5.0 | 10.9 | 2.5 |
Agilent 0 gap | 4953642 | 89.8 | 74.1 | 2.3 | 18.2 | 0.3 | 2.9 | 0.5 | 1.7 |
Agilent 20 gap | 4052727 | 88.3 | 74.8 | 2.8 | 17.3 | 0.4 | 2.6 | 0.6 | 1.5 |
Agilent | 9006369 | 89.1 | 74.4 | 2.5 | 17.8 | 0.3 | 2.8 | 0.6 | 1.6 |
Custom Array 12K | 5195976 | 87.3 | 70.1 | 1.7 | 21.2 | 0.1 | 3.9 | 0.7 | 2.3 |
Comparison[edit]
Comparison of Errors
Comparing errors per 100 bp
Insertions/Deletions (/100 bp) | Substitutions (/100 bp) | |
Mycroarray | 1.20 | 0.74 |
Agilent | 0.08 | 0.48 |
Custom Array 12K | 0.05 | 0.60 |
Comparison by Error
Y axis is given in % chance, so Agilent probes have overall error rate of ~2%, or 1 in 50 bp.
File:AgilentMYCA ErrorComp090313.png
Probe Counts Comparison[edit]
Looking at the comparison between counts of the three companies. Bar graphs below divide the probes into 4 categories: zero, under-amplified, normally amplified, and over-amplified. All counts are normalized to the expected number of reads. Expected number of reads is calculated by dividing the total number of reads by the total number of probes in the set. The expected number of reads is therefore the number of reads if all probes were amplified equally. Under amplified probes are defined as those with less than half the number of expected reads. This is because PCR amplifies at 2^n. Having half as many reads is therefore the same as the probe being amplified one less cycle than the norm. Similarly, over-amplified is defined as having more than twice the number of reads. Again, having twice as many reads is the same as saying the probe was amplified for one extra cycle.
The four categories are:
Zero: The probe was never counted
Under Amplified: probe count < 0.5*expected
Normally Amplified: 0.5*expected ≤ probe count ≤ 2*expected
Over-amplified: probecount > 2*expected
Probe Count Comparison