Mercurial > repos > saskia-hiltemann > virtual_normal_analysis
diff README.txt @ 0:1209f18a5a83 draft
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author | saskia-hiltemann |
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date | Mon, 03 Aug 2015 05:01:15 -0400 |
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children | 885ba15c2564 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.txt Mon Aug 03 05:01:15 2015 -0400 @@ -0,0 +1,32 @@ +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.