Workflows for RNA-Seq analysis

There are:

Last update: 2020-06-18

This is a RNA-Seq analysis workflow including transcripts assembly for paired-end sequencing data.

It contains:

Environments and dependencies:

RNASeq.yml
- snakemake (v5.7.4)
- HISAT2 (v2.2.0)
- samtools (v1.9)
- StringTie (v2.1.1)
py27.yml
- python (v2.7.15)

All you need:

Create an environment with RNASeq.yml and activate it, or use your own pacakges
A sample_list.txt containing all the sample names separated by comma (e.g. SRR9048143,SRR9048144)
An annotation file (e.g. Mus_musculus.GRCm38.96.gtf)
Genome index for HISAT2
Put the paired fastq files of each sample into datasets
prepDE.py file for generating counts matirx
Edit RNASeq.sanke:
- Assign GENOME_GTF = "PATH_TO_YOUR_ANNOTATION_FILE"
- Assign HISAT2_INDEX_PREFIX = "PATH_TO_GENOME_INDEX(contain index prefix)"

Usage: snakemake --use-conda -p -j {threads} -s RNASeq.snake

Last update: 2020-04-24

This is a RNA-Seq analysis workflow for read counting for paired-end sequencing data.

It contains:

Environments and dependencies:

All you need:

Create an environement with RNASeq.yml and activate it, or use your own packages
A sample_list.txt containing all the sample names separated by comma (e.g. SRR9048143,SRR9048144)
An annotation file (e.g. Mus_musculus.GRCm38.96.gtf)
Genome index for HISAT2
Put the paired fastq files of each sample into datasets
Edit RNASeq.sanke:
- Assign GENOME_GTF = "PATH_TO_YOUR_ANNOTATION_FILE"
- Assign HISAT2_INDEX_PREFIX = "PATH_TO_GENOME_INDEX(contain index prefix)"

Usage: snakemake -p -j {threads} -s RNASeq_Counts.snake

Last update: 2020-08-31

This is a command line executable script for counts to RPKM/FPKM and TPM transformation and annotations using ENSEMBL datasets.

Usage: Rscript counts_to_tpm.R {input} {species} {output}

input: it takes the output count matirx of featureCounts. e.g. counts.txt from the pipeline
species: it supports human and mouse. Default: human
output: set for output filename. Default: GeneExpression.txt