stringtie

There are 0 repository under stringtie topic.

• cfarkas / annotate_my_genomes

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

  transcriptome-assemblytranscriptomegenome-annotationrna-seqstringtiebraker2
  Language:Nextflow 30

• PavlidisLab / rnaseq-pipeline

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

  rna-seqalignmentquantificationngsngs-analysisilluminarsemstarstringtiefastqcbioinformatics-pipelinebioinformaticsgene-expressiontranscriptomicsgenomicsspliced-alignmentsplice-awarebash
  Language:Shell 24

• 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.

  transcriptomehisat2deseq2oysterstringtie
  Language:R 3

• 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

  rnaseq-pipelinehisat2stringtietranscriptome-assemblydifferential-gene-expression
  Language:Shell 3

• jlanga / smsk_tuxedo2

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

  ballgowncondaconda-environmentdifferentialexpressionhisat2rrna-seqrnaseqrskittlebrewersamtoolssmsksnakemakestringtietuxedo2
  Language:Python 1

• 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

  htseq-countsnakemakefastqsstarpipelineballgownstringtieslurm-cluster
  Language:R 1

• Animesh911 / Project-lncRNA

  stringtieballgownhisat2noiseqnew-tuxedo-protocol
  0

• 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.

  assembly-toolscufflinksdifferentially-expressed-genesfastphisat2mapping-toolsrna-seq-analysisrna-seq-pipelinesamtoolsstringtie
  Language:Shell 0