Nextflow Alignment Pipeline - from fastq.gz to sorted bam/cram with ease

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.

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

SPEAQeasy: portable LIBD RNA-seq pipeline using Nextflow. Check http://research.libd.org/SPEAQeasy-example/ for an example on how to use this pipeline and analyze the resulting output files.

Single-end RNA-seq pipeline: FastQC → Trimmomatic → HISAT2 → featureCounts. 93.98% alignment rate.

Cell-surface glycoRNA-based cancer detection.

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

Analysis of .fastq ChIP-seq datasets

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

RNA-seq analyses.

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.

Guide for aligning reads to a reference genome with HISAT2.

Bioinformatics Programming - Transcriptome Assembly

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

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

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

Quality Control, Mapping and Reads Count for RNA-Seq Analysis

VAP : For Reference mapping and Variant detection.

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

This repository houses the pipeline I coded to perform differential analysis of transcriptomes from two oyster species, C. gigas and C. virginica and isolate genes in the apoptosis pathway.