Daniel:Notebook/GenomeMiner: Difference between revisions
Jump to navigation
Jump to search
>Djacobse (→HL155) |
>Djacobse (→HL155) |
||
Line 21: | Line 21: | ||
Analysis of 3 probe production companies: MYcroarray, Agilent, and Custom Array. | Analysis of 3 probe production companies: MYcroarray, Agilent, and Custom Array. | ||
'''Raw Data''' ([[Daniel:Notebook/GenomeMiner/2013-8-13|Dan | '''Raw Data''' Methods: ([[Daniel:Notebook/GenomeMiner/2013-8-13|Dan]],[[Matt:LabNotes/2013-8-9|Matt]]) | ||
{| class="wikitable" <hiddentext>generated with [[:de:Wikipedia:Helferlein/VBA-Macro for EXCEL tableconversion]] V1.8</hiddentext> | {| class="wikitable" <hiddentext>generated with [[:de:Wikipedia:Helferlein/VBA-Macro for EXCEL tableconversion]] V1.8</hiddentext> | ||
|- style="font-size:12pt;font-weight:bold" | |- style="font-size:12pt;font-weight:bold" |
Revision as of 00:02, 14 August 2013
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.
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 |
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 |