stringtie

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.

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

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 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.

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 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.

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.