@@ -96,8 +96,7 @@ The columns must be separated by a tablulation.
| --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 |
| --min_avg_coverage | Minimum coverage a transcript must have to \
be considered | float | 0.5 |
| --min_avg_coverage | Minimum coverage a transcript must have to be considered | float | 0.5 |
| --nt_wrap | The number of nucleotides right before or right after the CDS of transcript to display the the coverage figure. Important note : The transcripts having their 5'UTR or 3'UTR smaller than this number wont be considered | int | 50 |
| --ci | The size of cofidence interval to display for each bin. You can set it to 0 to hide the confidence interval. The confidence interval is built by resampling the coverage values of transcripts at each bin with replacement. The mean value is then calculated. The process is repeated 1000 times and it's one those value that the confidence interval is computed | int | 0 |
