:78 Function create_function() is deprecated [8192]
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diff --git a/README b/README index 227db41..3c701e1 100644 --- a/README +++ b/README @@ -68,9 +68,10 @@ RACS | âââ test | âââ lst âââ datasets - |  âââ - |  âââ - |  âââ + |  âââ PostProcessing_Genic.xlsx + |  âââ PostProcessing_Intergenic.xlsx + | âââ IBD1_ORF.xlsx + |  âââIBD1_Intergenic.xlsx âââ hpc â  âââ submission.pbs |  âââ submission.slurm @@ -350,9 +351,28 @@ Additionally one could adjust the following variables: III) normalization and cut-off with negative control +We provide a shell script that can be used for normalizing and dealing with the +cut-offs when your data includes wild-types or negative controls. +The script can be found in the core directory, and is named "normalizeORG.sh". +It requires 3 arguments: + - 1st argument: "FINAL.table.*" file from RACS' ORF pipeline + - 2nd argument: "PF-INPUT-value" PF value correspoding to the INPUT file + - 3rd argument: "PF-IP-value" PF value correspoding to the IP file + - 4th argument: 'A' or 'D' (OPTIONAL), when this 4th argument is specified, an additional table is created being ordered with respect to the IP/INPUT ratio, in "A"scending or "D"ecreasing order -IV) normalization and cut-off without a negative control + PATHtoRACS/core/normalizeORF.sh FINAL.table.XXXX 14694464 10148171 + PATHtoRACS/core/normalizeORF.sh FINAL.table.XXXX 14694464 10148171 A + +Alternatively one could use a couple of spreadsheets available in the 'datasets' +directory, if the user prefers to proceed in an interactive manner. +See, + datasets/PostProcessing_Genic.xlsx + datasets/PostProcessing_Intergenic.xlsx -V) comparison to MACS and XXXX +IV) normalization and cut-off without a negative control + --- in prep. --- + +V) comparison to MACS and Other Tools + --- in prep. ---