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LBMC
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hic
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f54bf1e1
Commit
f54bf1e1
authored
5 years ago
by
nservant
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update README
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@@ -39,6 +39,28 @@ sites (bowtie2)
6.
Quality controls and report (MultiQC)
7.
Addition export for visualisation and downstream analysis (cooler)
## Quick Start
i. Install
[
`nextflow`
](
https://nf-co.re/usage/installation
)
ii. Install one of
[
`docker`
](
https://docs.docker.com/engine/installation/
)
,
[
`singularity`
](
https://www.sylabs.io/guides/3.0/user-guide/
)
or
[
`conda`
](
https://conda.io/miniconda.html
)
iii. Download the pipeline and test it on a minimal dataset with a single command
```
bash
nextflow run hic
-profile
test
,<docker/singularity/conda>
```
iv. Start running your own analysis!
```
bash
nextflow run hic
-profile
<docker/singularity/conda>
--reads
'*_R{1,2}.fastq.gz'
--genome
GRCh37
```
See
[
usage docs
](
docs/usage.md
)
for all of the available options when running the pipeline.
## Documentation
The nf-core/hic pipeline comes with documentation about the pipeline, found in
...
...
@@ -53,6 +75,16 @@ the `docs/` directory:
4.
[
Output and how to interpret the results
](
docs/output.md
)
5.
[
Troubleshooting
](
https://nf-co.re/usage/troubleshooting
)
## Contributions and Support
If you would like to contribute to this pipeline, please see the
[
contributing guidelines
](
.github/CONTRIBUTING.md
)
.
For further information or help, don't hesitate to get in touch on
[
Slack
](
https://nfcore.slack.com/channels/hic
)
.
You can join with
[
this invite
](
https://nf-co.re/join/slack
)
.
## Credits
nf-core/hic was originally written by Nicolas Servant.
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