| Literature DB >> 30956140 |
Joel Rozowsky1, Robert R Kitchen1, Jonathan J Park1, Timur R Galeev1, James Diao2, Jonathan Warrell1, William Thistlethwaite3, Sai L Subramanian3, Aleksandar Milosavljevic3, Mark Gerstein4.
Abstract
Small RNA sequencing has been widely adopted to study the diversity of extracellular RNAs (exRNAs) in biofluids; however, the analysis of exRNA samples can be challenging: they are vulnerable to contamination and artifacts from different isolation techniques, present in lower concentrations than cellular RNA, and occasionally of exogenous origin. To address these challenges, we present exceRpt, the exRNA-processing toolkit of the NIH Extracellular RNA Communication Consortium (ERCC). exceRpt is structured as a cascade of filters and quantifications prioritized based on one's confidence in a given set of annotated RNAs. It generates quality control reports and abundance estimates for RNA biotypes. It is also capable of characterizing mappings to exogenous genomes, which, in turn, can be used to generate phylogenetic trees. exceRpt has been used to uniformly process all ∼3,500 exRNA-seq datasets in the public exRNA Atlas and is available from genboree.org and github.gersteinlab.org/exceRpt.Entities:
Keywords: RNA sequencing; RNA-seq; bioinformatics; bioinformatics tool; exRNAs; extracellular RNA; genomics; pipeline; transcriptome
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Year: 2019 PMID： 30956140 PMCID： PMC7079576 DOI： 10.1016/j.cels.2019.03.004
Source DB: PubMed Journal: Cell Syst ISSN： 2405-4712 Impact factor: 10.304