Skip to content
Snippets Groups Projects
Commit cdc84f75 authored by nservant's avatar nservant
Browse files

[DOC] update usage

parent df5a0243
No related branches found
No related tags found
No related merge requests found
......@@ -185,7 +185,7 @@ NXF_OPTS='-Xms1g -Xmx4g'
### Hi-C digestion protocol
Here is an command line example for standard DpnII digestion protocols.
Alignment will be performed on the `mm10` genome with default paramters.
Alignment will be performed on the `mm10` genome with default parameters.
Multi-hits will not be considered and duplicates will be removed.
Note that by default, no filters are applied on DNA and restriction fragment sizes.
......@@ -250,13 +250,13 @@ run the pipeline:
### `--bwt2_index`
The bowtie2 indexes are required to run the Hi-C pipeline. If the
The bowtie2 indexes are required to align the data with the HiC-Pro workflow. If the
`--bwt2_index` is not specified, the pipeline will either use the igenome
bowtie2 indexes (see `--genome` option) or build the indexes on-the-fly
(see `--fasta` option)
```bash
--bwt2_index '[path to bowtie2 index (with basename)]'
--bwt2_index '[path to bowtie2 index]'
```
### `--chromosome_size`
......@@ -305,7 +305,7 @@ file with coordinates of restriction fragments.
If not specified, this file will be automatically created by the pipline.
In this case, the `--fasta` reference genome will be used.
Note that the `--restriction_site` parameter is mandatory to create this file.
Note that the `digestion` or `--restriction_site` parameter is mandatory to create this file.
## Hi-C specific options
......@@ -313,7 +313,7 @@ The following options are defined in the `nextflow.config` file, and can be
updated either using a custom configuration file (see `-c` option) or using
command line parameter.
### Reads mapping
### HiC-pro mapping
The reads mapping is currently based on the two-steps strategy implemented in
the HiC-pro pipeline. The idea is to first align reads from end-to-end.
......@@ -398,6 +398,22 @@ Default: 'AAGCTAGCTT'
Exemple of the ARIMA kit: GATCGATC,GANTGATC,GANTANTC,GATCANTC
### DNAse Hi-C
#### `--dnase`
In DNAse Hi-C mode, all options related to digestion Hi-C
(see previous section) are ignored.
In this case, it is highly recommanded to use the `--min_cis_dist` parameter
to remove spurious ligation products.
```bash
--dnase'
```
### HiC-pro processing
#### `--min_restriction_fragment_size`
Minimum size of restriction fragments to consider for the Hi-C processing.
......@@ -434,21 +450,6 @@ Default: '0' - no filter
--max_insert_size '[numeric]'
```
### DNAse Hi-C
#### `--dnase`
In DNAse Hi-C mode, all options related to digestion Hi-C
(see previous section) are ignored.
In this case, it is highly recommanded to use the `--min_cis_dist` parameter
to remove spurious ligation products.
```bash
--dnase'
```
### Hi-C processing
#### `--min_cis_dist`
Filter short range contact below the specified distance.
......@@ -479,16 +480,42 @@ Note that in this case the `--min_mapq` parameter is ignored.
## Genome-wide contact maps
Once the list of valid pairs is available, the standard is now to move on the `cooler`
framework to build the raw and balanced contact maps in txt and (m)cool formats.
### `--bin_size`
Resolution of contact maps to generate (space separated).
Default:'1000000,500000'
Resolution of contact maps to generate (comma separated).
Default:'1000000'
```bash
--bins_size '[numeric]'
--bins_size '[string]'
```
### `--ice_max_iter`
### `--res_zoomify`
Define the maximum resolution to reach when zoomify the cool contact maps.
Default:'5000'
```bash
--res_zoomify '[string]'
```
### HiC-Pro contact maps
Note that by default, the contact maps are now generated with the `cooler` framework.
However, for backward compatibility, the raw and normalized maps can still be generated
by HiC-pro if the `--hicpro_maps` parameter is set.
#### `--hicpro_maps
If specified, the raw and ICE normalized contact maps will be generated by HiC-Pro.
```bash
--hicpro_maps
```
#### `--ice_max_iter`
Maximum number of iteration for ICE normalization.
Default: 100
......@@ -497,7 +524,7 @@ Default: 100
--ice_max_iter '[numeric]'
```
### `--ice_filer_low_count_perc`
#### `--ice_filer_low_count_perc`
Define which pourcentage of bins with low counts should be force to zero.
Default: 0.02
......@@ -506,7 +533,7 @@ Default: 0.02
--ice_filter_low_count_perc '[numeric]'
```
### `--ice_filer_high_count_perc`
#### `--ice_filer_high_count_perc`
Define which pourcentage of bins with low counts should be discarded before
normalization. Default: 0
......@@ -515,7 +542,7 @@ normalization. Default: 0
--ice_filter_high_count_perc '[numeric]'
```
### `--ice_eps`
#### `--ice_eps`
The relative increment in the results before declaring convergence for ICE
normalization. Default: 0.1
......@@ -524,6 +551,54 @@ normalization. Default: 0.1
--ice_eps '[numeric]'
```
## Downstream analysis
### Additional quality controls
#### `--res_dist_decay`
Generates distance vs Hi-C counts plots at a given resolution using HiCExplorer
Several resolution can be specified (comma separeted). Default: '250000'
```bash
--res_dist_decay '[string]'
```
### Compartment calling
Call open/close compartments for each chromosome, using the `cooltools` command.
#### `--res_compartments`
Resolution to call the chromosome compartments (comma separated).
Default: '250000'
```bash
--res_compartments '[string]'
```
### TADs calling
#### `--tads_caller`
TADs calling can be performed using different approaches.
Currently available options are 'insulation' and 'hicexplorer'.
Note that all options can be specified (comma separated).
Default: 'insulation'
```bash
--tads_caller '[string]'
```
#### `--res_tads`
Resolution to run the TADs calling analysis (comma separated).
Default: '40000'
```bash
--res_tads '[string]'
```
## Inputs/Outputs
### `--split_fastq`
......@@ -578,13 +653,13 @@ genome-wide maps are not built. Usefult for capture-C analysis. Default: false
--skip_maps
```
### `--skip_ice`
### `--skip_balancing`
If defined, the ICE normalization is not run on the raw contact maps.
If defined, the contact maps normalization is not run on the raw contact maps.
Default: false
```bash
--skip_ice
--skip_balancing
```
### `--skip_cool`
......@@ -595,6 +670,30 @@ If defined, cooler files are not generated. Default: false
--skip_cool
```
### `skip_dist_decay`
Do not run distance decay plots. Default: false
```bash
--skip_dist_decay
```
### `skip_compartments`
Do not call compartments. Default: false
```bash
--skip_compartments
```
### `skip_tads`
Do not call TADs. Default: false
```bash
--skip_tads
```
### `--skip_multiQC`
If defined, the MultiQC report is not generated. Default: false
......
0% Loading or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment