@@ -169,10 +169,10 @@ All results are available in `results/hicpro/stats`.
**Output directory: `results/hicpro/stats`**
-*mapstat - mapping statistics per read mate
-*pairstat - R1/R2 pairing statistics
-*RSstat - Statitics of number of read pairs falling in each category
-*mergestat - statistics about duplicates removal and valid pairs information
*\*mapstat - mapping statistics per read mate
*\*pairstat - R1/R2 pairing statistics
*\*RSstat - Statitics of number of read pairs falling in each category
*\*mergestat - statistics about duplicates removal and valid pairs information
#### Contact maps
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@@ -192,15 +192,15 @@ is specified on the command line.
**Output directory: `results/hicpro/matrix`**
-`*.matrix` - genome-wide contact maps
-`*_iced.matrix` - genome-wide iced contact maps
*`*.matrix` - genome-wide contact maps
*`*_iced.matrix` - genome-wide iced contact maps
The contact maps are generated for all specified resolutions
(see `--bin_size` argument).
A contact map is defined by :
- A list of genomic intervals related to the specified resolution (BED format).
- A matrix, stored as standard triplet sparse format (i.e. list format).
* A list of genomic intervals related to the specified resolution (BED format).
* A matrix, stored as standard triplet sparse format (i.e. list format).
Based on the observation that a contact map is symmetric and usually sparse,
only non-zero values are stored for half of the matrix. The user can specified
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@@ -254,8 +254,8 @@ Here, we use the implementation available in the [`cooltools`](https://cooltools
Results are available in **`results/compartments/`** folder and includes :
-`*cis.vecs.tsv`: eigenvectors decomposition along the genome
-`*cis.lam.txt`: eigenvalues associated with the eigenvectors
*`*cis.vecs.tsv`: eigenvectors decomposition along the genome
*`*cis.lam.txt`: eigenvalues associated with the eigenvectors
### TADs calling
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@@ -266,8 +266,8 @@ TADs calling remains a challenging task, and even if many methods have been prop
Currently, the pipeline proposes two approaches :
- Insulation score using the [`cooltools`](https://cooltools.readthedocs.io/en/latest/cli.html#cooltools-diamond-insulation) package. Results are availabe in **`results/tads/insulation`**.
-[`HiCExplorer TADs calling`](https://hicexplorer.readthedocs.io/en/latest/content/tools/hicFindTADs.html). Results are available at **`results/tads/hicexplorer`**.
* Insulation score using the [`cooltools`](https://cooltools.readthedocs.io/en/latest/cli.html#cooltools-diamond-insulation) package. Results are availabe in **`results/tads/insulation`**.
*[`HiCExplorer TADs calling`](https://hicexplorer.readthedocs.io/en/latest/content/tools/hicFindTADs.html). Results are available at **`results/tads/hicexplorer`**.
Usually, TADs results are presented as simple BED files, or bigWig files, with the position of boundaries along the genome.
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@@ -276,10 +276,10 @@ Usually, TADs results are presented as simple BED files, or bigWig files, with t
<detailsmarkdown="1">
<summary>Output files</summary>
-`multiqc/`
-`multiqc_report.html`: a standalone HTML file that can be viewed in your web browser.
-`multiqc_data/`: directory containing parsed statistics from the different tools used in the pipeline.
-`multiqc_plots/`: directory containing static images from the report in various formats.
*`multiqc/`
*`multiqc_report.html`: a standalone HTML file that can be viewed in your web browser.
*`multiqc_data/`: directory containing parsed statistics from the different tools used in the pipeline.
*`multiqc_plots/`: directory containing static images from the report in various formats.
</details>
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@@ -292,10 +292,10 @@ Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQ
<detailsmarkdown="1">
<summary>Output files</summary>
-`pipeline_info/`
- Reports generated by Nextflow: `execution_report.html`, `execution_timeline.html`, `execution_trace.txt` and `pipeline_dag.dot`/`pipeline_dag.svg`.
- Reports generated by the pipeline: `pipeline_report.html`, `pipeline_report.txt` and `software_versions.yml`. The `pipeline_report*` files will only be present if the `--email` / `--email_on_fail` parameter's are used when running the pipeline.
- Reformatted samplesheet files used as input to the pipeline: `samplesheet.valid.csv`.
*`pipeline_info/`
* Reports generated by Nextflow: `execution_report.html`, `execution_timeline.html`, `execution_trace.txt` and `pipeline_dag.dot`/`pipeline_dag.svg`.
* Reports generated by the pipeline: `pipeline_report.html`, `pipeline_report.txt` and `software_versions.yml`. The `pipeline_report*` files will only be present if the `--email` / `--email_on_fail` parameter's are used when running the pipeline.
* Reformatted samplesheet files used as input to the pipeline: `samplesheet.valid.csv`.