LEADER 04125nam 22005535 450 001 9910337570903321 005 20200701155807.0 010 $a3-030-13973-5 024 7 $a10.1007/978-3-030-13973-5 035 $a(CKB)4100000007758157 035 $a(MiAaPQ)EBC5723083 035 $a(DE-He213)978-3-030-13973-5 035 $a(PPN)23523267X 035 $a(EXLCZ)994100000007758157 100 $a20190301d2019 u| 0 101 0 $aeng 135 $aurcnu|||||||| 181 $ctxt$2rdacontent 182 $cc$2rdamedia 183 $acr$2rdacarrier 200 10$aHidden Treasures in Contemporary RNA Sequencing /$fby Serghei Mangul, Harry Taegyun Yang, Eleazar Eskin, Noah Zaitlen 205 $a1st ed. 2019. 210 1$aCham :$cSpringer International Publishing :$cImprint: Springer,$d2019. 215 $a1 online resource (99 pages) 225 1 $aSpringerBriefs in Computer Science,$x2191-5768 311 $a3-030-13972-7 327 $aAbstract -- Main Text -- Acknowledgement -- Disclosure -- References. 330 $aAdvances in RNA-sequencing (RNA-seq) technologies have provided an unprecedented opportunity to explore the gene expression landscape across individuals, tissues, and environments by efficiently profiling the RNA sequences present in the samples. When a reference genome sequence or a transcriptome of the sample is available, mapping-based RNA-seq analysis protocols align the RNA-seq reads to the reference sequences, identify novel transcripts, and quantify the abundance of expressed transcripts. The reads that fail to map to the human reference, known as unmapped reads, are a large and often overlooked output of standard RNA-seq analyses. Even in carefully executed experiments, the unmapped reads can comprise a considerable fraction of the complete set of reads produced, and can arise due to technical sequencing produced by low-quality and error-prone copies of the nascent RNA sequence being sampled. Reads can also remain unmapped due to unknown transcripts, recombined B and T cell receptor sequences, A-to-G mismatches from A-to-I RNA editing, trans-splicing, gene fusion, circular RNAs, and the presence of non-host RNA sequences (e.g. bacterial, fungal, and viral organisms). Unmapped reads represent a rich resource for the study of B and T cell receptor repertoires and the human microbiome system?without incurring the expense of additional targeted sequencing. This book introduces and describes the Read Origin Protocol (ROP), a tool that identifies the origin of both mapped and unmapped reads. The protocol first identifies human reads using a standard high-throughput algorithm to map them onto a reference genome and transcriptome. After alignment, reads are grouped into genomic (e.g. CDS, UTRs, introns) and repetitive (e.g. SINEs, LINEs, LTRs) categories. The rest of the ROP protocol characterizes the remaining unmapped reads, which failed to map to the human reference sequences. 410 0$aSpringerBriefs in Computer Science,$x2191-5768 606 $aBioinformatics 606 $aGenetics 606 $aComputational Biology/Bioinformatics$3https://scigraph.springernature.com/ontologies/product-market-codes/I23050 606 $aBioinformatics$3https://scigraph.springernature.com/ontologies/product-market-codes/L15001 606 $aGenetics and Genomics$3https://scigraph.springernature.com/ontologies/product-market-codes/L32000 615 0$aBioinformatics. 615 0$aGenetics. 615 14$aComputational Biology/Bioinformatics. 615 24$aBioinformatics. 615 24$aGenetics and Genomics. 676 $a547.79 676 $a572.8633 700 $aMangul$b Serghei$4aut$4http://id.loc.gov/vocabulary/relators/aut$01060298 702 $aYang$b Harry Taegyun$4aut$4http://id.loc.gov/vocabulary/relators/aut 702 $aEskin$b Eleazar$4aut$4http://id.loc.gov/vocabulary/relators/aut 702 $aZaitlen$b Noah$4aut$4http://id.loc.gov/vocabulary/relators/aut 906 $aBOOK 912 $a9910337570903321 996 $aHidden Treasures in Contemporary RNA Sequencing$92512314 997 $aUNINA