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.
journal_name
Cell Systjournal_title
Cell systemsauthors
Rozowsky J,Kitchen RR,Park JJ,Galeev TR,Diao J,Warrell J,Thistlethwaite W,Subramanian SL,Milosavljevic A,Gerstein Mdoi
10.1016/j.cels.2019.03.004subject
Has Abstractpub_date
2019-04-24 00:00:00pages
352-357.e3issue
4eissn
2405-4712issn
2405-4720pii
S2405-4712(19)30074-2journal_volume
8pub_type
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