README modification

README.md

@@ -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
+```
\ No newline at end of file