STRST: STAR and Trinity RNA-seq Tool

Pipelines for RNA-seq analysis: STAR and Trinity. This package using two approaches for RNA-seq a) STAR and b) Trinity. The package includes the data cleaning, alignment/assembly, DE/Annotation analysis and data visualization for GO.

please find more detail for STAR and Trinity-wiki in the links below: STAR: https://github.com/alexdobin/STAR Trinity: https://github.com/trinityrnaseq/trinityrnaseq/wiki

Environment setup

It is better to run this package in virtual environment. Set up the virtual environment with following steps:

0. Install virtualenv

$ pip3 install virtualenv 

1. Setup virtualenv

$ python3 -m venv venv 

2. Activate virtualenv

$ source ./venv/bin/activate

After setting up virtualenv, install

3. Install package

$ pip install -e .

Usage guidance

Functions include in the package:

📝 Function explain - function name

1. Pre-alignment quality control - fastqc
2. Trimmed adapter - trimmed_adapter
3. Prepare genome for STAR alignment - star_genome_prep
4. STAR alignment - star_alignment 🚧
5. Post STAR alignment - quality control 🚧
6. Prepare files for post STAR alignment - prepare_bamfiles_postqc 🚧
7. Count the Transcripts - htseq_count 🚧
8. Trinity assembly - trinity_assemble
9. Estimate the expression after Trinity assembly - trinity_estimate_expression
10. Calculate the transcripts and transfer into a matrix - trinity_abundance_estimates_to_matrix
11. Trinity DE analysis - trinity_run_de_analysis
12. RNA-seq data visualization - trinity_run_glimma 🚧

Pre-alignment quality control (fastqc)

🚧 under construction

RNA-seq alignment/assembly

🚧 under construction

post-alignment quality control

🚧 under construction

RNA-seq data visualization

🚧 under construction

Functional analysis

🚧 under construction