Page Comparison

Overview

• Similar to exercise 6.4 we will:

  • Use created “samplesheet.csv” metadata file for small RNAseq datasets in exercise 6.4.

  • Use a “nextflow.config” file in the working directory to override Nextflow parameters (e.g., specify where to find the pipeline assets).

  • Use a PBS script to run the expression profiling of miRNAs against MirGeneDB, a curated database that includes experimentally validated miRNAs.

Prepare pipeline inputs

Let’s move to the working directory:

...

cat launch_nf-core_smallRNAseq_MirGeneDB.pbs

...

TIP: when running the nf-core/smrnaseq pipeline (release 2.3.1) the pipeline is not able to find the location of the reference adapter sequences for trimming of the raw small RNAseq pipeline, so we need to specify where to find the folder where the adapter sequences file is located. To do this, we prepare a “nextflow.config” file (see below). This file should be already in your working directory. Print the content as follows:

cat nextflow.config

singularity {
    runOptions = '-B $HOME/.nextflow/assets/nf-core/smrnaseq/assets'
}

Note: if a config file is placed in the working folder it can override parameters define by the global ~/.nextflow/config file or the config file define as part of the pipeline.

Submit the job Submit the job to the HPC cluster:

qsub launch_nf-core_smallRNAseq_miRBaseMirGeneDB.pbs

Monitor the progress:

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Note: the “mature_counts.csv” needs to be transposed prior running the statistical analysis. This can be done either user the R script or using a script called “transpose_csv.py”.

Let’s copy the transpose_csv.py script to the working folder:

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