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
git clone
Change into the dada directory:
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
mkdir DATA
## Overview
## 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
"SAMPLES": ["SRR5625858"],
"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
gzip SRR5625858
At this point you have all the data needed to run the pipeline.
**Run dada**
./ global.smk
\ No newline at end of file
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment