diff --git a/README.md b/README.md index ee46f10..01b1186 100644 --- a/README.md +++ b/README.md @@ -148,9 +148,10 @@ In both formats, the `--contigs` argument should specify a FASTA file containing Binette results are stored in the `results` directory. You can specify a different directory using the `--outdir` option. In this directory you will find: -- `final_bins_quality_reports.tsv`: This is a TSV (tab-separated values) file containing quality information about the final selected bins. -- `final_bins/`: This directory stores all the selected bins in fasta format. -- `temporary_files/`: This directory contains intermediate files. If you choose to use the `--resume` option, Binette will utilize files in this directory to prevent the recomputation of time-consuming steps. +- **`final_bins_quality_reports.tsv`**: This is a TSV (tab-separated values) file containing quality information about the final selected bins. +- **`final_bins/`**: This directory stores all the selected bins in fasta format. +- **`input_bins_quality_reports/`**: A directory storing quality reports for the input bin sets, with files following the same structure as `final_bins_quality_reports.tsv`. +- **`temporary_files/`**: This directory contains intermediate files. If you choose to use the `--resume` option, Binette will utilize files in this directory to prevent the recomputation of time-consuming steps. The `final_bins_quality_reports.tsv` file contains the following columns: diff --git a/docs/tutorial/analyse_binette_result.ipynb b/docs/tutorial/analyse_binette_result.ipynb index 94d1fc8..f1d9586 100644 --- a/docs/tutorial/analyse_binette_result.ipynb +++ b/docs/tutorial/analyse_binette_result.ipynb @@ -7,7 +7,9 @@ "source": [ "## Analyse Binette results\n", "\n", - "Let's visualize the results from Binette and compare them to the initial bin sets used as input. " + "Let's visualize the results from Binette and compare them to the initial bin sets used as input. \n", + "\n", + "To explore these results interactively, you can open the Jupyter notebook via Binder by following this link: [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/genotoul-bioinfo/Binette/binder_tutorial_env?urlpath=git-pull%3Frepo%3Dhttps%253A%252F%252Fgithub.com%252Fgenotoul-bioinfo%252FBinette%26urlpath%3Dtree%252FBinette%252Fdocs%252Ftutorial%252Fanalyse_binette_result.ipynb%26branch%3Dmain)" ] }, { @@ -31,7 +33,8 @@ "from pathlib import Path\n", "import plotly.express as px\n", "\n", - "# This is needed to properly display Plotly graphs in the documentation\n", + "# The following two lines are needed to properly display Plotly graphs in the documentation\n", + "# However you may need to remove these lines and restart the kernel to visualise the graph in another context\n", "import plotly.io as pio\n", "pio.renderers.default = \"sphinx_gallery\"" ] @@ -949,7 +952,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.8.19" + "version": "3.8.12" } }, "nbformat": 4, diff --git a/docs/tutorial/get_dataset.md b/docs/tutorial/get_dataset.md index f099b17..ac55c7f 100644 --- a/docs/tutorial/get_dataset.md +++ b/docs/tutorial/get_dataset.md @@ -24,7 +24,7 @@ Once the tool is installed, you can download the "Kickstart" dataset with the fo ```{code-block} bash # Select the header of the table - head -n7 coal-metagenomics.tsv > coal-metagenomics_Kickstart_only.tsv + head -n8 coal-metagenomics.tsv > coal-metagenomics_Kickstart_only.tsv # Append the relevant line for the Kickstart dataset grep SRR5058924 coal-metagenomics.tsv >> coal-metagenomics_Kickstart_only.tsv