RNA-seq analyses.

Nextflow Alignment Pipeline

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.

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.

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.

Evaluating HISAT2, Salmon and Kallisto alignment using Checkpoint Blockade treated CT26 Experimental Data

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

Codes that I use for day-to-day work in lab.

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

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

A pre-processing (alignment) pipeline based on hisat2