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

RNA-seq analyses.

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.

VAP : For Reference mapping and Variant detection.

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.

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

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.

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

Scripts to index and align Bovine genome with HISAT2

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

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

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.

A pre-processing (alignment) pipeline based on 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.

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

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

Bioinformatics Programming - Transcriptome Assembly

Nextflow Alignment Pipeline