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Analysis of RNA-Seq Data Using TopHat and Cufflinks

The recent advances in high throughput RNA sequencing (RNA-Seq) have generated huge amounts of data in a very short span of time for a single sample. These data have required the parallel advancement of computing tools to organize and interpret them meaningfully in terms of biological implications, at the same time using minimum computing resources to reduce computation costs. Described here is the method of analyzing RNA-seq data using the set of open source software programs of the Tuxedo suite: TopHat and Cufflinks. TopHat is designed to align RNA-seq reads to a reference genome, while Cufflinks assembles these mapped reads into possible transcripts and then generates a final transcriptome assembly. Cufflinks also includes Cuffdiff, which accepts the reads assembled from two or more biological conditions and analyzes their differential expression of genes and transcripts, thus aiding in the investigation of their transcriptional and post transcriptional regulation under different conditions. Also ...

November 4th, 2015|Analysis Pipelines|
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The Application of RNA Sequencing in Systemic Lupus Erythematosus

Summary RNA sequencing (RNA-seq) has emerged as a powerful tool for gene expression analysis, allowing for the comprehensive study of the transcriptome. It has become an essential technique in various research fields, including disease research. Here, we will explore how RNA-seq was applied to investigate the mechanism of synaptic stripping by microglia in a mouse model of lupus. This study, from Nanjing Drum Tower Hospital collaborated with Nanjing University of Chinese Medicine titled, "Neuronal NR4A1 deficiency drives coordinated synaptic stripping by microglia in a mouse model of lupus"[1] , used RNA-seq and other research methods to clarify that synaptic loss is the early pathology of lupus brain injury, and microglia, complement signals and neurons participate in this process. Background Systemic lupus erythematosus (SLE) is an autoimmune disease that is difficult to cure. 40-90% of SLE patients experience neuropsychiatric symptoms, known as neuropsychiatric lupus erythematosus (NPSLE)[2,3]. The early pathogenesis of NPSEL ...

March 24th, 2025|Publications, User Submitted Posts|
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ARPIR – automatic RNA-Seq pipelines with interactive report

RNA-Seq is an increasing used methodology to study either coding and non-coding RNA expression. There are many software tools available for each phase of the RNA-Seq analysis and each of them uses different algorithms. Furthermore, the analysis consists of several steps regarding alignment (primary-analysis), quantification, differential analysis (secondary-analysis) and any tertiary-analysis and can therefore be time-consuming to deal with each step separately, in addition to requiring a computer knowledge. For this reason, the development of an automated pipeline that allows the entire analysis to be managed through a single initial command and that is easy to use even for those without computer skills can be useful. Faced with the vast availability of RNA-Seq analysis tools, it is first of all necessary to select a limited number of pipelines to include. For this purpose, University of Perugia researchers compared eight pipelines obtained by combining the most used tools and for each one ...

January 29th, 2021|Analysis Pipelines, Data Analysis, Methods, Technology, Workflows|
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scFlowReport: A Reproducible Workflow for Comparative Downstream Biological Analysis of Single-Cell RNA-seq Data
scLTF: A self-training clustering framework for large-scale single-cell RNA-Seq data

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