@@ -90,8 +90,8 @@ Example of the content in the design file:
...
@@ -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) |
| `-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) |
| `-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)|
| ` -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 |
| `-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 |
| `-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) |
| ` -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:
The figure to give to the `--norm` parameter must be defined like this:
