Commit f2a6b988 authored by peguerin's avatar peguerin
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readme update

parent 942981b9
......@@ -69,13 +69,13 @@ singularity pull --name seaconnect.simg shub://Grelot/..........................
## Preprocessing
First, SINGLE-END `fastq` files must be quality-filtered.
We provide a complete workflow to perform preprocessing of sequencing ngs raw data. This workflow is available as a github repositories here : [clean-fastq](https://github.com/Grelot/clean-fastq)
We provide a complete workflow to perform preprocessing of sequencing ngs raw data. This workflow is available as a github repository here : [clean-fastq](https://github.com/Grelot/clean-fastq)
## Set up
### Wildcards
* `{species}` : any complete project (in our case we have 2 projects : mullus and diplodus)
* `{species}` : any complete project (in our case we have 2 projects : _mullus_ and _diplodus_)
* `{lane}` : any physical lane on a flow cell that goes into the sequencing machine. We have many `{lane}` by `{species}`
* `{barcode}` : any DNA sequence attached to a reads which belong to a sample. We have many `{barcode}` by `{lane}` by `{species}`
* `{pop}` : any group of samples
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