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Cedric Midoux
deepomics16S
Commits
aa3868fa
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aa3868fa
authored
Mar 24, 2021
by
Slaheddine Kastalli
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README modification
parent
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@@ -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

## 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
SRR
5625858
```
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
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