A genome annotation pipeline that use short and long sequencing reads alignments from animal genomes

RNA-seq pipeline for raw sequence alignment and transcript/gene quantification.

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.

This is an automated workflow pipeline for analyzing and processing Bulk-RNA seq data, implemented primarily in bash, python and R, and wrapped in a NextFlow workflow to characterize the gene landscape in the samples.

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

Immunopeptidogenomics pipeline that builds a cryptic peptide database from RNA-seq and identifies non-canonical (cryptic) peptides in immunopeptidomics mass spectrometry data.

Attempt at snakemake pipeline. Pyflow was forked from https://github.com/crazyhottom but the Snakefile infrastructure and rule calling was inspired by https://github.com/snakemake-workflows

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

This is an automated workflow pipeline for analyzing and processing Bulk-RNA seq data, implemented primarily in bash, python and R, and wrapped in a NextFlow workflow to characterize the gene landscape in the samples.

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.