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bioRxiv · 10.1101/836973

A Simplest Bioinformatics Pipeline for Whole Transcriptome Sequencing: Overview of the Processing and Steps from Raw Data to Downstream Analysis.

Gupta, A.·Gupta, S.·Jatawa, S. K.·Mishra, A. K.·Suravajhala, P.
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Abstract

Recent advances in next generation sequencing (NGS) technologies have heralded the genomic research. From the good-old inferring differentially expressed genes (DEG) using microarray to the current adage NGS-based whole transcriptome or RNA-Seq pipelines, there have been advances and improvements. With several bioinformatics pipelines for analysing RNA-Seq on rise, inferring the candidate DEGs prove to be a cumbersome approach as one may have to reach consensus among all the pipelines. To Check this, we have benchmarked the well known cufflinks-cuffdiff pipeline on a set of datasets and outline it in the form of a protocol where researchers interested in performing whole transcriptome shotgun sequencing and its downstream analysis can better disseminate the analysis using their datasets.

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Gupta, A., Gupta, S., Jatawa, S. K., Mishra, A. K., Suravajhala, P.. 2019-11-09. A Simplest Bioinformatics Pipeline for Whole Transcriptome Sequencing: Overview of the Processing and Steps from Raw Data to Downstream Analysis.. https://doi.org/10.1101/836973

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