Fall 2022. DSCI512 RNA Sequencing Data Analysis. This is a pipeline to assist students with single-end RNA-seq data in their analysis
DSCI512 - RNA sequencing data analysis - course scripts
A simple set of wrappers and tools for RNA-seq analysis. These tools were designed for the DSCI512 RNA-seq analysis class at Colorado State University
This set of pipelines are specifically designed for students who want to use single-end short read sequencing data.
To obtain the repository of scripts
- Navigate into your project directory and to your subdirectory called 02_scripts
- Use git clone as shown below to pull the information from github to your location on SUMMIT
$ cd /scratch/summit/<eID>@colostate.edu #Replace <eID> with your EID
$ cd PROJ05_ExamProject
$ cd 02_scripts
$ git clone <paste path to github repository here>To explore what you obtained
Notice that instead of having a single script, you now have a few scripts. These will work in a Two step method for executing jobs on summit. The execute script calls the analyze script. This Readme file and a license file were also downloaded.
Let's copy the two scripts up one directory. This will create duplicate copies for you to edit on and will move the scripts directly into ''02_scripts'', not its sub-directory.
$ cd 2022_DSCI512_RNAseq_singleend
$ cp execute_RNAseq_pipeline.sbatch ..
$ cp RNAseq_single_analyzer_220624.sh
$ cp RNAseq_cleanup_220615.sh ..
$ cd ..- Prepare a metadata file in which:
- The first column is the .fastq file
- The second column is blank
- The third column is a nickname in the form NN01
- The fourth column is a nickname with some information about the conditions like NN01_cond1_cond2_rep1
- The next columns keep track of the different conditions
- the last column is the replicate #
Example of a metadata file:
#SRR10398489.fastq CYSL01 01_N2_ribo_1 N2 riboseq 1 #SRR10398490.fastq CYSL02 02_N2_ribo_2 N2 riboseq 2 #SRR10398491.fastq CYSL03 03_N2_ribo_3 N2 riboseq 3 #SRR10398492.fastq CYSL04 04_meg34_ribo_1 meg34 riboseq 1 #SRR10398493.fastq CYSL05 05_meg34_ribo_2 meg34 riboseq 2 #SRR10398494.fastq CYSL06 06_meg34_ribo_3 meg34 riboseq 3 #SRR10398495.fastq CYSL07 07_N2_mRNA_1 N2 mRNA 1 #SRR10398496.fastq CYSL08 08_N2_mRNA_2 N2 mRNA 2 #SRR10398497.fastq CYSL09 09_N2_mRNA_3 N2 mRNA 3 #SRR10398498.fastq CYSL10 10_meg34_mRNA_1 meg34 mRNA 1 #SRR10398499.fastq CYSL11 11_meg34_mRNA_2 meg34 mRNA 2 #SRR10398500.fastq CYSL12 12_meg34_mRNA_3 meg34 mRNA 3
Note - You'll need to write this yourself based on the infomration you can obtain from the paper or the SRA Archive information.
- Amend the #SBATCH commands
- With the execute script, add the path to your metadata file
- Within the analyze script, amend the Modify This Section part
- Execute the script like so...
$ sbatch execute execute_RNAseq_pipeline.sbatch