denovo-rnaseq

Description

• This is a simple Snakemake workflow to perform de novo transcriptome assembly, DGE, and annotation.
• The workfow currently annotates the highly differential expressed genes with PVal of 0.005 and log_fold_change of 1.

Create conda enviornment

conda env create -f environment.yml
conda activate rnaseq

Limitations

• This workflow is meant to be easy to run, fast to implement, so it's currently not supporting flexibile configs.
• If you need to change configuration and parameters you will need to edit the Snakefile.
• It's only supporting RNASeq paired-end gzipped samples (not interleaved).

Main software used

• Error trimming: fastp
• De novo transcriptome assembly: rnaSpades
• Quantification: Salmon
• Differential gene expression: DESEQ2
• Annotation: Trinotate

How to use?

1. Create a working directory
2. Change the ROOT_DIR in the Snakefile to match your working directory.
3. Create a directory with the name samples inside the working directory.
4. Put your samples in the samples directory with the naming convection:
   • R1: <sample_name>_1.fastq.gz
   • R2: <sample_name>_2.fastq.gz
5. Copy paste the tab-delimited file samples.tsv in your workflow directory.
6. Modify the samples.tsv to match your samples. Columns as following (sample_type, sample_name, R1_path, R2_path).

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You may use the following bash commands to update the Snakefile and samples.tsv files.

curr=$(pwd)/workflow/
sed -i "s/REPLACE_ABSOLUTE_PATH/${curr//\//\\/}/g" workflow/samples.tsv
sed -i "s/REPLACE_ROOT_DIR/${curr//\//\\/}/g" Snakefile

Workflow rulegraph