Raw reads analysis

DEG-Differentially Expressed Genes (1) Align reads to reference using HISAT2 aligner (2) HTSeq-Count (3) DESeq2

Isoform-level differential expression analysis (1) Align reads to reference using HISAT2 aligner (2) Assemble transcripts with StringTie-1.3.3 (3) Merge all StringTie-1.3.3 transcripts into a single transcriptome annotation file using StringTie-1.3.3_merge (4) Create Ballgown input files using with StringTie-1.3.3 (5) Compare expression analysis using Ballgownseq

R workflows

RNA-seq workflow: gene-level exploratory analysis and differential expression https://bioconductor.org/help/workflows/rnaseqGene/