Commit aa3868fa authored by Slaheddine Kastalli's avatar Slaheddine Kastalli
Browse files

README modification

parent 34b26177
......@@ -9,8 +9,55 @@ First we clone the git repository, in your line command go to your working direc
```bash
git clone https://forgemia.inra.fr/cedric.midoux/dada2.git
```
Change into the dada directory:
```bash
cd dada2
```
At this point, you have all the scripts you need to run the workflow using snakemake, and you'd just need to get some data.
Create a folder called DATA into the dada2 directory
```bash
mkdir DATA
```
## Overview
![Image](save_home/skastalli/dada2/report/global_graph.pdf)
## Steps of dada2
* primer removal - using preprocess
* quality filtering and trimming - using preprocess
* learn the error rates - using dada2
* sample inference - using dada2
* construct the sequence table - using dada2
* chimera removal - using dada2
* track reads through the pipeline - using dada2
## Running snakemake manually
Once you have all the files, edit the config.json file with your raw fastq
* Example
````json
{
"THREADS": 1,
"SAMPLES": ["SRR5625858"],
"FIVE_PRIMER": {"SRR5625858": "GTGYCAGCMGCCGCGGTA"},
"THREE_PRIMER": {"SRR5625858": "ACTYAAAKGAATTGRCGGGG"},
"DATABASE": "/db/frogs_databanks/assignation/16S/silva_132_16S_pintail100/silva_132_16S_pintail100.fasta"
}
```
the fastq files must be located in the DATA folder and gz format.
In your terminal use this command
```shell
gzip SRR5625858
```
At this point you have all the data needed to run the pipeline.
**Run dada**
```shell
./qsubSnake.sh global.smk
```
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