Commit 7e1d1dd3 authored by Andre Gohr's avatar Andre Gohr
Browse files

now accepts species with underscore like Homo_sapiens

parent d6652033
......@@ -43,7 +43,7 @@ Options:
--betaprior <boolean> Apply betaprior when running DESeq2 [default: TRUE]
--sub_data <boolean> Subset de_results by contrasts and store the data in a subfolder [default: FALSE]
--gtf <gtf_file> Path to a GTF file, preferably the same used for read counting.
--genic_counts <genic_file> Path to a the genic counts file. this should the file *.complete_table.txt generated with dge_workflow/genic_counts.R, but it can be any file that contains three columns named: _ensembl_gene_id_, _sample_, and _nonexonic_ratio_. Sample names should match those of the input count table.
--genic_counts <genic_file> Path to a the genic counts file. this should the file *.complete_table.txt generated with dge_workflow/genic_counts.R, but it can be any file that contains three columns named: _ensembl_gene_id_, _sample_, and _nonexonic_ratio_. Sample names should match those of the input count table.
'
#commandArgs <- function(x) c("--design", "'batch+condition'", "--contrasts", "../contrasts.txt star_counts_matrix_reduced_sampleset.txt", "basic_design_reduced_sampleset.txt")
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