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Commit 47e95831 authored by nservant's avatar nservant
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[DOC] update usage.md

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......@@ -195,8 +195,7 @@ NXF_OPTS='-Xms1g -Xmx4g'
Here is an command line example for standard DpnII digestion protocols.
Alignment will be performed on the `mm10` genome with default paramters.
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.
Note that by default, no filters are applied on DNA and restriction fragment sizes.
```bash
nextflow run main.nf --input './*_R{1,2}.fastq.gz' --genome 'mm10' --digestion 'dnpii'
......@@ -209,7 +208,7 @@ Alignment will be performed on the `mm10` genome with default paramters.
Multi-hits will not be considered and duplicates will be removed.
Contacts involving fragments separated by less than 1000bp will be discarded.
```
```bash
nextflow run main.nf --input './*_R{1,2}.fastq.gz' --genome 'mm10' --dnase --min_cis 1000
```
......
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