Overview

LrRNAseq GAST processes BLAST alignments of full length long read RNAseq transcripts to a relatively short genomic region (e.g. 100kb) and facilitates recognition of gene splicing.

The lrRNAseq_GAST_visualiser.ipynb is the main notebook used for visualisation of collective BLAST alignments (pseudo Global alignment).

The bioinformatic_functions.ipynb is required to be imported in the main file to call multiple functions from.

The rest of the files serve as example data to try out.

Requirements

• Jupyter Notebook or Jupyter Lab
• Python libraries: Pandas, Matplotlib, Numpy, Regex, Biopython, OS, ast, operator
• seqtk installed via bioconda i.e. conda install bioconda::seqtk