stringtie
There are 8 repositories under stringtie topic.
cfarkas/annotate_my_genomes
A genome annotation pipeline that use short and long sequencing reads alignments from animal genomes
PavlidisLab/rnaseq-pipeline
RNA-seq pipeline for raw sequence alignment and transcript/gene quantification.
erinwitkop/apoptosis_data_pipeline
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.
mppl1/RNAseq_preprocessing
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
jlanga/smsk_tuxedo2
snakemake files of the tuxedo v2 pipeline from Pertea et al 2016
Manninm/MiKTMCSnakemakePipeline
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
groverkaushal/RNAseq-Workflow-Mapping-Assembly-and-Differential-Gene-Expression-Analysis
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.