Independent project I undertook to perform a full ChIP-Seq analysis of the transcription factor Nanog in Zebrafish embryos.

This project uses an workflow pipeline to generate map and assemble RNAseq reads to a reference genome. Furthermore, we generate counts data and identify differentially expressed genes from 2 conditions.

A pre-processing (alignment) pipeline based on hisat2

A tool for generating and processing nucleotide conversion tables from HISAT-3N alignment results.

rna-seq pipeline for drosophila melanogaster: qc, trimming, alignment, and read counting (81.7% alignment, ~50m bp processed)

Comprehensive bioinformatics workflow for RNA-seq quality control, trimming, alignment, and gene quantification. Automates the complete pipeline from raw FASTQ to gene expression counts using FastQC, FASTP, HISAT2, and featureCounts.

RNA-Seq pipelines that use HISAT2, Kallisto, Salmon, DESeq and Sleuth.

Investigating unmapped reads within next generation sequencing data will provide additional information regarding the source of the trace microbial reads.

Proof of concept of a RNA-Seq pipeline from reads to count matrix (including quality control) with Nextflow and additional example RNA-Seq analysis in R

Bioinformatics Programming - Transcriptome Assembly

Repository for bulk RNA-seq analyses (from undergrad 2nd-3rd year) – Reorganized

Cell-surface glycoRNA-based cancer detection.

Analysis of .fastq ChIP-seq datasets

Bulk RNA-seq Nextflow pipeline: FastQC, fastp, HISAT2, featureCounts, DESeq2, MultiQC. Dockerised, tested, reproducible.

Scripts to index and align Bovine genome with HISAT2

A front-end GUI to map NGS DNA sequencing data using HISAT backend tool. This software offers robust seamless queueing of the mapping operations along with parameter memory for quick and easy customization.

snakemake files of the tuxedo v2 pipeline from Pertea et al 2016

Guide for aligning reads to a reference genome with HISAT2.

Build Docker container for HISAT2 and (optionally) convert to Apptainer/Singularity.