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Preprocessing

The preprocessing step involves searching for full length transcripts from raw basecalled reads.

First, basecalled ONT reads are filtered by the minimum read quality using Filtlong. Then, full length transcripts are found using Pychopper.

Usage

Input - RawData/X.fastq

Output - Results/Pychopper/X.pychop.fastq

Configuration

Below are changes that can be configured in the config.yaml file or explicitly specified in the command line.

Filtlong

min_mean_q: 5 - Minimum read quality.

Pychopper

porechop_heu_stringency: 0.25 - Stringency of porechop heuristic.

Output Folder Structure

| -- FilteredData/
    | -- X.fastq
    ...
| -- Results/
    | -- Pychopper/
        | -- X.pychop.fastq
        ...