EAN: 9783030139728

SPRINGERBRIEFS IN COMPUTER SCIENCE HIDDEN TRE...

Advances 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.

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