Correcting Isoform Reads

The transcriptome step involves correcting isoform reads from the de novo based transcriptome.

Gffcompare is used to compare transcripts to the existing annotation to determine any potential redundant reads.

This part of the pipeline is primarly based on the ont_tutorial_pinfish released by Nanopore Technologies.

Usage

Input -

/path/to/genome/fasta/X.fa
Results/Pychopper/X.pychop.fastq

Output - Results/Gffcompare/nanopore.combined.gtf

snakemake

Configuration

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

Gffcompare

Output Folder Structure

| -- Results/
    | -- Pinfish/
        | -- corrected_transcriptome_polished_collapsed.fas
        | -- corrected_transcriptome_polished_collapsed_nonred.fas
    | -- Gffcompare/
        | -- nanopore.combined.gtf
        ...