Acclimabest

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

1. Trancriptome assembly

1.1 Raw data trimming

00_scripts/datarmor_jobs/01_transcriptome_assembly/01_trimmomatic_jobs_pe.sh

Make sure that you are in the root of the git repository

1.2 Prepare reference

qsub 00_scripts/01_transcriptome_assembly/02_gmap_index.sh 

1.3 Filtering datasets assembly

This step is meant to tease apart host from symbionts transcripts (i.e Corals, Giant clams,..)

00_scripts/datarmor_jobs/01_transcriptome_assembly/03_gmap_mapping_jobs.sh

00_scripts/datarmor_jobs/01_transcriptome_assembly/04_clean_dataset_jobs.sh

1.4 Assemble the transcriptome

qsub 00_scripts/datarmor_jobs/05_merge_input.sh

qsub 00_scripts/datarmor_jobs/06_assemble_trinity.sh

1.5 Assembly statistics

qsub 00_scripts/datarmor_jobs/07_assembly_stats

1.6 Assembly filtering

2. Differential expression analysis

2.1 Raw data trimming

00_scripts/datarmor_jobs/02_diff_expression/01_trimmomatic_jobs_pe.sh

Make sure that you are in the root of the git repository

2.2 Prepare reference

qsub 00_scripts/02_diff_expression/02_gmap_index.sh

2.3 Filtering datasets assembly

This step is meant to tease apart host from symbionts transcripts (i.e Corals, Giant clams,..)

00_scripts/datarmor_jobs/02_diff_expression/03_gmap_mapping_jobs.sh

00_scripts/datarmor_jobs/02_diff_expression/04_clean_dataset_jobs.sh

2.4 Mapping

00_scripts/datarmor_jobs/02_diff_expression/05_gsnap_mapping_jobs.sh

2.5 Counting gene expression

00_scripts/datarmor_jobs/02_diff_expression/06_htseq_count.sh

2.6 Differential expression testing

3. WGCNA

in progress

4. SNPs

in progress

Prerequisities

BBmap

GMAP/GSNAP

samtools

seqtk

sra-tools

Trimmomatic

Trinity

UniVec

Flow chart

Contributors

Alves Monteiro Kisalu Homère e-mail: homere.alves-monteiro-kisalu@edu.mnhn.fr

Brahmi Chloé e-mail: chloe.brahmi@upf.pf

Le Luyer Jérémy e-mail: jeremy.le.luyer@ifremer.fr