| --normalization | The normalization method to apply on the transcript. See deeptools documentation to chose the normalization method (it can take the following values RPKM, CPM, BPM, RPGC, None) | string | CPM |
| --pool_file | A file used to pool samples together the number of categories of transcripts you want to create. You can enter `None` if you don't want to pull samples together| File, string | None |
| --transcript_group_number | The number of transcript groups you want to have. One coverage figure will be created for each transcript group | int | 5 |
| --transcript_group_number | The number of transcript groups you want to have. One coverage figure will be created for each transcript group. A group of transcript corresponds to transcripts with similar size. | int | 5 |
| --bin_numbers | The number of bin we want to use for each category of transcript. You can entrer '-1' to automatically compute a number of bins a category of transcript. If you have 3 group of transcript and you whant to set 20 bins for the smallest transcripts, 30 bins for the medium transcripts and 40 bins for the largest you can entrer | string | "-1" |
| --trim | The proportion of the smallest and largest transcripts to remove. You can enter 0.025 to remove 2.5% of the smallest and largest transcript or 0 to not remove anything | float | 0.025
| --project_name | Name of the project, used in result file names | string | metatranscript_analysis |
