Softwares that can be used for each step of RNA-seq data analysis:

Mohammad Shahbaz Khan @Mohammad-Shahbaz-Khan

01 January 1970 0 9K Report

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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