Daniel:Notebook/GenomeMiner

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Revision as of 20:00, 14 August 2013 by >Djacobse
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Link to useful Perl website: Basic Perl

Calendar

<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

Raw Data Methods: (Dan,Matt)

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

File:Probecompare HL155.png


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:ProbeComparison Improved.png