diff --git a/docs/usage.md b/docs/usage.md index cbaab42923f1be0eb13e7490b2263359b3f25d7f..be630a4298976e67bec49659f6dc6bc38ac86cc6 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -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 ```