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changes.mady.by.user Roberto Barrero Gumiel

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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)

Code Block
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:

Code Block
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:

Code Block
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

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