Assembly of RNA transcriptome, differential expression analysis, identification of lncRNA candidates based on genomic context and protein coding potential.

Visualize read-to-contig alignment during assembly analysis

an investigation into the efficiency of Trinity transcriptome assemblies

Scripts and notes related to the manuscript: Stuart KC & Edwards RJ et al. 2022. Transcript- and annotation-guided genome assembly of the European starling. Molecular Ecology Resources, doi.org/10.1101/2021.04.07.438753. † joint first author

Bioinformatics Programming - Transcriptome Assembly

a_inornata research project

Snakemake workflow to de novo assemble transcriptomes with two software, Trinity and Shannon. Imported from my GitLab.

Material used for a course on transcriptomics, covering transcriptome assembly, transcriptome functional annotation, differential expression analysis, and functional annotation data mining

To perform RNA-Seq data analysis and calculate length-scaled transcripts per million (TPM) values using the Salmon tool and the GenomicFeatures package in R.

These are tutorials on a subset of tools available for processing raw RNAseq data. This if for HISAT2_SAMtools_Stringtie_gffcompare_ballgown pipeline or HISAT2_SAMtools_Stringtie_PrepDEanalysis.py_DESeq2 pipeline

Cleavage site prediction via de novo assembly

A collection of scripts for our PacBio paper

The AugusMake pipeline is a Snakemake-based workflow for generating gene annotations using the Augustus software. AugusMake can perform gene predictions using any combination of the three methods: ab initio, with extrinsic hints, or by training a new species.

Supplementay Material for publication "Species-specific molecular responses of wild coral reef fishes during a marine heatwave"

from trinity assembly to deep learning

QuantEval is an analysis pipeline which evaluate the reliability of quantification tools.

tool for long read transcriptome assembly

Finding putative exons and constructing splicegraphs using Trans-ABySS contigs

A collection of scripts for our PacBio paper

Assembler for multiple RNA-seq samples