Commit 1037d2ee authored by peguerin's avatar peguerin
Browse files

readme update

parent 20cb1b29
......@@ -155,7 +155,7 @@ This command process demultiplexing for each `{lane}`. Results are stored into `
:warning: If your cleaned fastq data folder is not into the current directory, you have to create a binding point for the singularity container. Modify the `--singularity-args "-B /entrepot:/entrepot"` argument of the command below.
## _(optional)_ Blacklisting samples with low coverage
## :paperclip: _(optional)_ Blacklisting samples with low coverage
If you want a blacklist of `{sample}` fastq files with low coverage, you can use [DEMORT](https://pypi.org/project/demort/0.2.4/) to get number of reads by `{sample}` fastq files.
```
......@@ -174,7 +174,7 @@ bash 00-scripts/rename.sh {species} 01-infos/{species}_sample_information.csv 98
This command create a symlink of all fastq files such as `03-samples/{lane}/sample_{barcode}.fq.gz` is linked by `04-ddocent/{species}/{pop}_{sample}.F.fq.gz`.
:paperclip: Optionally, if a samples blacklist is provided, each blacklisted {sample} is filtered.
:paperclip: Optionally, if a samples blacklist `98-utils/{species}_samples_blacklist.txt` is provided, each blacklisted `{sample}` is filtered.
## dDocent workflow
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