5. RNA-seq pipeline

Overview

Use modified launch script to run the full pipeline, including trimming parameters based on the QC output.
Inspect precomputed results

Run full nf-core/rnaseq pipeline

STEP1: copy metadata (sample sheet.csv) into the working folder (run2_RNAseq)

cp $HOME/workshop/2024-2/session4_RNAseq/data/mouse/samplesheet.csv $HOME/workshop/2024-2/session4_RNAseq/runs/run2_RNAseq
cd $HOME/workshop/2024-2/session4_RNAseq/runs/run2_RNAseq

Line 1: Copy the samplesheet.csv file to the working directory
Line 2: move to the working directory

Copy the PBS Pro script to run the nf-core/rnaseq pipeline:

cp $HOME/workshop/2024-2/session4_RNAseq/scripts/launch_nf-core_RNAseq_pipeline.pbs $HOME/workshop/2024-2/session4_RNAseq/runs/run2_RNAseq

NOTE: if you had issues with the above lines. Alternatively, run the following code to copy the sample sheet.csv and launch files:

cp /work/training/2024/rnaseq/data/samplesheet.csv $HOME/workshop/2024-2/session4_RNAseq/runs/run2_RNAseq
cp /work/training/2024/rnaseq/scripts/launch_nf-core_RNAseq_pipeline.pbs
cd $HOME/workshop/2024-2/session4_RNAseq/runs/run2_RNAseq

Adjusting the Trim Galore (read trimming) options

Print the content of the launch_RNAseq.pbs script:

Submitting the job

Monitoring the Run

Outputs

The pipeline will produce two folders, one called “work,” where all the processing is done, and another called “results,” where we can find the pipeline's outputs. The content of the results folder is as follows:

The quantification of the gene and transcript expressions can be found in the ‘star_salmon’ directory.

The following feature count tables are generated: