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 |
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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 |
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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. You can run the following code to copy the sample sheet.csv and launch script from a shared folder:
| Code Block |
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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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