Daniel:Notebook/GenomeMiner
Jump to navigation
Jump to search
Link to useful Perl website: Basic Perl
<calendar> name=Daniel:Notebook/GenomeMiner format=%name/%year-%month-%day date=2013/02/01 view=oneyear </calendar>
Useful Linux Commands
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
HL155
Analysis of 3 probe production companies: MYcroarray, Agilent, and Custom Array.
Raw Data
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
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 |