TY - JOUR T1 - XPRESSyourself: Enhancing and Automating the Ribosome Profiling and RNA-Seq Analysis Toolkit JF - bioRxiv DO - 10.1101/704320 SP - 704320 AU - Jordan A. Berg AU - Jonathan R. Belyeu AU - Jeffrey T. Morgan AU - Alex J. Bott AU - Yeyun Ouyang AU - Aaron R. Quinlan AU - Jason Gertz AU - Jared Rutter Y1 - 2019/01/01 UR - http://biorxiv.org/content/early/2019/07/16/704320.abstract N2 - Nucleic acid sequencing is a powerful research tool that has become routine; however, computational bottlenecks hinder many users. XPRESSyourself is a ribosome profiling and RNA-Seq analytical pipeline that aims to eliminate these barriers, standardize in silico protocols, and decrease time-to-discovery. XPRESSyourself additionally introduces tools missing from current ribosome profiling and RNA-Seq toolkits. Using XPRESSyourself to process publicly available ribosome profiling data, we were able to rapidly identify hypothetical mechanisms related to neurodegenerative phenotypes and neuroprotective mechanisms of the small-molecule ISRIB during acute cellular stress, highlighting the ability of XPRESSyourself to rapidly uncover novel biological insight from high-throughput sequence data.BAMBinary Sequence Alignment MapBEDBrowser Extensible DatacDNAcomplementary DNACDScoding sequence of gene ChIP-seqchromatin immunoprecipitation sequencingCPUcentral processing unitdbGaPDatabase of Genotypes and PhenotypesDNAdeoxyribonucleic acidFDRfalse discovery rateFPKMfragments per kilobase of transcript per millionGEOGene Expression OmnibusGTFGeneral Transfer FormatIGVIntegrative Genomics ViewerISRintegrated stress responseISRIBISR inhibitormRNAmessenger RNAntnucleotidePCAprincipal component analysisPCRpolymerase chain reactionRAMrandom access memoryRNAribonucleic acidRNA-SeqRNA sequencingRPKMreads per kilobase of transcript per millionRPMreads per millionrRNAribosomal RNATCGAThe Cancer Genome AtlasTEtranslation efficiencyTPMtranscripts per millionUMIunique molecular identifierUTRuntranslated region ER -