balharbi/epigenetics_workflow

Pipeline for RRBS data analysis without a reference genome

#Epigenetics_workflow

Worflow for epigenetics methylation analysis whithout a reference genome

WARNING

The software is provided "as is", without warranty of any kind, express or implied, including but not limited to the warranties of merchantability, fitness for a particular purpose and noninfringement. In no event shall the authors or copyright holders be liable for any claim, damages or other liability, whether in an action of contract, tort or otherwise, arising from, out of or in connection with the software or the use or other dealings in the software.

Documentation

Note that ALL the scripts must be launched from the root folder rna-seq_mapping_workflow/

1. Clone git hub directory

git clone https://github.com/jleluyer/epigenetics_workflow

2. Import data

cp /path/to/the/data/repository/*.gz 02_data

3. Trimming the data

First you need to change the userID and userEmail for your proper info in ./00_scripts/colosse-jobs/01_trimmomatic_pe.sh

Then launch:

sbatch 00_scripts/katak-jobs/01_trim_galore.sh

You may also want to check the quality of your data prior to trimming using 00_scripts/utility_scripts/fastq.sh. This will require to have fastQC installed in your $PATH.

4. Create reference catalog

• Launch Ustacks

sbatch 00_scripts/02_ustacks_jobs.sh

• Launch Cstacks

sbatch 00_scripts/03_cstacks_jobs.sh

Note: prior to launch the scripts, you will need to adapt the values (-M, -m and -N and -n, for ustacks and cstacks, respectively)

5. Mapping

• Prepare reference genome

sbatch 00_scripts/04_prepare_reference.sh

• Index reference

sbatch 00_scripts/05_bismark_index.sh

• Mapping on reference genome

sbatch 00_scripts/06_bismark_align.sh

6. Methylation calls

sbatch 00_scripts/07_bismark_CpG_extractor.sh

7. Downstream analysis

7.1 SNPs calling

Import BS-SNPer

git clone https://github.com/hellbelly/BS-Snper
cd BS-Snper-master
sh BS-Snper.sh

launch BS-SNPer

sbatch 00_scripts/11_bssnper.sh

Notes

Dependencies

Softwares

Bismark

Trim_galore!

FastQC

STACKS

BS-SNPer

Licence

##Citations

F. Krueger, S. R. Andrews (2011). Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications doi: 10.1093/bioinformatics/btr167

J. M. Catchen, A. Amores, P. Hohenlohe. W.Cresko, J. H. Postlethwai (2011). Stacks: guilding and genotyping loci de novo from short-read sequences doi: 10.1534/g3.111.000240

G. Shengjie, Z. Dan, M. Likai, et al. BS-SNPer: SNP calling in bisulfite-seq data. Bioinformatics, 2015, 31(24): 4006-4008.doi: 10.1093/bioinformatics/btv507

worflow in progress

Contributors: Jeremy Le Luyer, Eric Normandeau, Madoka Krick