Here are some examples of software that can be used for each step of RNA-seq data analysis:

  • Quality Control: FastQC, PRINSEQ, Sickle
  • Read Trimming: Trimmomatic, Cutadapt, AdapterRemoval
  • Alignment: STAR, HISAT2, TopHat
  • Quality Control of Alignment: Qualimap, RSeQC, Picard
  • Assembly: Trinity, Oases, Trans-ABySS
  • Quantification: RSEM, Kallisto, eXpress
  • Differential Expression Analysis: DESeq2, EdgeR, limma
  • Functional Annotation: Blast2GO, KEGG, Reactome
  • Pathway Analysis: KEGG Pathway, Reactome, Enrichr
  • Network Analysis: Cytoscape, STRING, ClueGO
  • Visualization: IGV, GenomeBrowse, JBrowse
  • Interpretation: GSEA, DAVID, IPA
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