TallyTriN documentation!

Long-read sequencing has become an increasingly popular tool for RNA sequencing that provides unprecedented insight into isoform, translocation and variant calling analysis.

TallyTriN is a collection of bulk and single-cell workflows that utilize Unique Molecular Identifiers (UMIs) synthesized using trimer blocks of nucleotides.

Workflows

Included within this repo are the follwing workflows:

• pipeline_count - a bulk RNA-seq workflow that facilitates the analysis of UMIs synthesised using trimer nucleoside blocks added to the 5’ and 3’ of the RNA molecule.

• pipeline_fusion - a bulk analysis pipeline for the analysis of fusion transcripts. It implements a strategy for removing chimeric artefacts and quantifies real genomic translocation at the RNA-seq level.

• pipeline_singlecell - a workflow that facilitates the analysis of scCOLOR-seq nanopore single-cell sequencing data, but with trimers added at the 5’ end of the RNA.

• pipeline_10X - a workflow that facilitates the analysis of 10X sequencing data.

Citation

The bioRxiv manuscript accompanying this code can be found here:

https://www.biorxiv.org/content/10.1101/2023.04.06.535911v1