TopHat/Cufflinks (Tuxedo Suite)

Overview

The Tuxedo Suite is a bioinformatics pipeline for RNA-seq analysis consisting of TopHat2 (splice-aware short-read aligner using Bowtie2) and Cufflinks (transcript assembly and quantification). It maps reads to a reference genome while accounting for splicing, quantifies transcript abundance, and compares expression across conditions.

Used by

• TopHat2/Bowtie2/Cufflinks (Tuxedo Suite) used for transcript mapping and quantification in the PIPseq pediatric precision oncology program at Columbia University Medical Center; relative gene expression was compared against a 124-transcriptome reference panel (13 blood, 20 liver, 24 kidney, 17 lung, 50 brain tissues) PMID:28007021.
• Used TopHat/Cufflinks pipeline for RNA-seq alignment and transcript quantification PMID:28373299

Notes

• TopHat2 aligns reads splice-aware using Bowtie2 as the underlying aligner.
• Cufflinks performs de novo transcript assembly and FPKM quantification.
• Used alongside FusionMap (applied to unmapped reads) in the PIPseq clinical RNA-seq pipeline.

Sources

This page was processed by entity-page-writer on 2026-05-15. - PMID:28373299

This page was processed by wiki-cli on 2026-05-14.