https://github.com/meeranhussain/rnaseq_degseq_snakemake_no-replicates
Workflow for differential gene expression analysis for non-replicate samples using DEGseq
https://github.com/meeranhussain/rnaseq_degseq_snakemake_no-replicates
differential-gene-expression rna-seq-analysis rna-seq-pipeline snakemake-workflow star-aligner
Last synced: 3 months ago
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Workflow for differential gene expression analysis for non-replicate samples using DEGseq
- Host: GitHub
- URL: https://github.com/meeranhussain/rnaseq_degseq_snakemake_no-replicates
- Owner: meeranhussain
- Created: 2024-02-11T10:13:58.000Z (over 1 year ago)
- Default Branch: main
- Last Pushed: 2024-02-11T10:44:32.000Z (over 1 year ago)
- Last Synced: 2025-01-08T08:47:23.528Z (5 months ago)
- Topics: differential-gene-expression, rna-seq-analysis, rna-seq-pipeline, snakemake-workflow, star-aligner
- Language: R
- Homepage:
- Size: 20.5 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# Differential Gene Expression Analysis for Samples with No Replicates
This guide provides steps to run an RNA_SEQ Snakemake file for performing differential gene expression analysis when samples have no replicates.
## Steps to Run RNA_SEQ Snakemake File
### Step 1: Make a Project Folder with Project_ID
Create a project folder and assign it a meaningful Project_ID.
### Step 2: Copy Files into Project Folder
Copy the following files into the project folder:
- `Snakefile`
- `DEGSeq_no_replicate_final.R`
- `create_combinations.R`
- `config.yaml`
- `Master_file.txt`
### Step 3: Create a Sub-folder "1_Data"
Inside the project folder, create a sub-folder named `1_Data`.
### Step 4: Copy Sample Files to 1_Data
Copy the sample files into the `1_Data` folder. Ensure that you replace hyphens (-) with underscores (_) in file names. For example, `Tumor-1_R1.fq.gz` should be renamed to `Tumor_1_R1.fq.gz`.
### Step 5: Create "Master_file.txt"
Create a file named `Master_file.txt` in the project folder. This file should specify the combinations and replicates. Refer to the example file provided for better clarity.
### Step 6: Use Config File to Add Additional Information
Utilize the `config.yaml` file to add any additional information required for the workflow.
#### Config.yaml Content for RNA_SEQ Snakemake Workflow
```yaml
# Enter organism name (Scientific name)
org: "Mus musculus"
# Enter Kegg organism code
org_code: "mmu"
# Specify Number of threads
threads: "15"
# Specify Combinations using "+" between combinations
combinations: "Tumor_Lung + Tumor_Liver + Lung_Liver"
# Reference Assembly version (Indexing command provided below)
reference: ""
```
##### Genome indexing using STAR
```bash
STAR --runMode genomeGenerate --genomeDir {index_dir_name} --genomeFastaFiles {path to ".fasta" file} --sjdbGTFfile {path to ".gtf" file} --sjdbOverhang 100 --runThreadN 10
```
### Step 7: Open Terminal in Project Folder
Navigate to the project folder in your terminal/command prompt.
### Step 8: Run Snakemake
Type the following command in the terminal:
```bash
snakemake --configfile=config.yaml --cores 5
```