Mercurial > repos > saskia-hiltemann > virtual_normal_analysis
view README.txt @ 1:1c6710924e80 draft
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author | saskia-hiltemann |
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date | Mon, 03 Aug 2015 05:03:16 -0400 |
parents | 1209f18a5a83 |
children | 885ba15c2564 |
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Installs VirtualNormal Correction Tool After installing this tool via admin panel, manually configure the following: 1) edit virtual_normal_correction.loc file - change "/path/to/hg18.crr" to the location of the Complete Genomics reference crr file on your system (can be downloaded from ftp://ftp.completegenomics.com/ReferenceFiles/ ) - change "/path/to/VN_genomes_varfiles_hg18.txt" to the location of the file containing the locations of all the Complete Genomics varfiles to be used as a virtual normal. This file should contain 1 file location per line, e.g. /path/to/normal-varfile-1 /path/to/normal-varfile-2 /path/to/normal-varfile-3 /path/to/normal-varfile-4 /path/to/normal-varfile-5 /path/to/normal-varfile-6 /path/to/normal-varfile-7 /path/to/normal-varfile-8 ... Varfiles can be in compressed or uncompressed form. For example, Complete Genomics' Diversity panel can be used. (can be downloaded from ftp://ftp2.completegenomics.com/) - change "/path/to/VN_genomes_junctionfiles_hg18.txt" to the location of the file containing the locations of all the Complete Genomics junctionfiles to be used as a virtual normal. This file should contain 1 file location per line. For example, Complete Genomics' Diversity panel can be used. (can be downloaded from ftp://ftp2.completegenomics.com/) 2) restart Galaxy for changes to take effect After this initial setup, additional normals can be added to the lists without having to restart Galaxy.