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ONT Processing Tutorial

The data used for tutorial is taken from the SG-NEx (Signapore Nanopore Expression) Project, and more information can be found here: SG-NEx.

Input

The working directory should be setup in the configuration file: outdir:/path/to/output. This directory will be used for data input and output.

Below is the the input file structure for .fastq files, and how it should be in the configuration file.

Input file structure:

| -- RawData/Fastq/
    | -- A549_r1_r3.fastq
    | -- A549_r2_r1.fastq
    | -- A549_r5_r3.fastq
    ...

Configuration file structure:

samples:
    A549_1: "A549_r1_r3"
    A549_2: "A549_r2_r1"
    A549_5: "A549_r5_r3"
    ...

Configuration Settings

Outside of the changing the external tool paths, here are some additional configuration settings to keep in mind of.

### General pipeline parameters:
basecalling: FALSE
preprocess: TRUE
annotation: TRUE
quantification: TRUE

Also, create a line-delimited file with a list of genes of interest. For the sake of example, can just create a file with the gene ABI2.

gene_file: "/home/annaldas/projects/isoform_analysis/genes.tab"
output_plots: "test.pdf"

Command

snakemake --snakefile /path/to/isotv/snakemake -j 32