diff --git a/README.md b/README.md index fd1c95fb07be1e0f3f043cc320087c1632a37e94..fdf396c1ef5ef9d493cb89352e42c6ecde8e7ab3 100644 --- a/README.md +++ b/README.md @@ -90,8 +90,8 @@ Example of the content in the design file: | `-N / --norm` | A number corresponding to a bin for which the coverage will become 1. 'None' for no normalisation (default 'None'). Note that this parameter can also take a file (description after this table) | | `-s / --show_replicates` | 'y' to create a figure showing the coverage for all replicates 'n' to display only the average coverage across the conditions defined in `-d / --design` parameter. (default y) | | ` -e / --environment` | A list of two integer. The first corresponds to the number of nucleotides to display around the genomic intervals of interest defined with the `-r / --region_beds` parameter and the second corresponds to the number of bins to use (default 0 0)| -| `-b / --border_name` | A list of two string. The name of the left and right border to display in the figures between the genomic intervals defined with the `-r / --region_beds` and their environment | -| `-o / --output` | Folder where the figures will be stored | +| `-b / --border_name` | A list of two string. The name of the left and right border to display in the figures between the genomic intervals defined with the `-r / --region_beds` and their environment (default '' '')| +| `-o / --output` | Folder where the figures will be stored (default .) | | ` -y / --ylim` | A list of two integer that corresponds to the y-axis range in the figure. (default None) | The figure to give to the `--norm` parameter must be defined like this: