Commit 3034b24e authored by Slaheddine Kastalli's avatar Slaheddine Kastalli
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README changes

parent 831cbf13
# DADA2 pipeline
DADA2 is a bioinformatics pipeline (Callahan et al., 2016). It consists of a series of steps to filter the raw sequences obtained through Illumina sequencing. The final step aims to obtain the taxonomy of the sequences that have been filtered in order to study the microbial community.
DADA2 is a pipeline based on dada2 (Callahan et al., 2016) R package which consists of a series of steps to filter the raw sequences obtained through Illumina sequencing. The final step aims to obtain the taxonomy of the sequences that have been filtered in order to study the microbial community.
## Getting ready
......@@ -17,7 +17,7 @@ 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
Create a folder called DATA in the dada2 directory
```bash
mkdir DATA
......@@ -50,7 +50,7 @@ Once you have all the files, edit the config.json file with your raw fastq
```
the fastq files must be located in the DATA folder and gz format.
the fastq files must be located in the DATA folder and with gz format.
In your terminal use this command
```shell
gzip SRR5625858
......@@ -60,5 +60,5 @@ 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
./RunSnake.sh global.smk
```
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