ArticleBMC genomics2015
What's in your next-generation sequence data? An exploration of unmapped DNA and RNA sequence reads from the bovine reference individual.
Article in BMC genomics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
18 citing papers in PubMed, 36 citations in OpenAlex.
- Another lesson from unmapped reads: in-depth analysis of RNA-Seq reads from various horse tissues.Journal of applied genetics · 2022Article
- Article
- Novel functional sequences uncovered through a bovine multiassembly graph.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Article
- Humic-acid-driven escape from eye parasites revealed by RNA-seq and target-specific metabarcoding.Parasites & vectors · 2020Article
- Comparative RNA-Seq transcriptome analyses reveal dynamic time-dependent effects ofBMC genomics · 2020Article
- CAFU: a Galaxy framework for exploring unmapped RNA-Seq data.Briefings in bioinformatics · 2020Article
- Exploring the unmapped DNA and RNA reads in a songbird genome.BMC genomics · 2019Article
- A comprehensive manually-curated compendium of bovine transcription factors.Scientific reports · 2018Article
- Assembly and Analysis of Unmapped Genome Sequence Reads Reveal Novel Sequence and Variation in Dogs.Scientific reports · 2018Article
- Study of the Metatranscriptome of Eight Social and Solitary Wild Bee Species Reveals Novel Viruses and Bee Parasites.Frontiers in microbiology · 2018Article
- Article
- Lessons for livestock genomics from genome and transcriptome sequencing in cattle and other mammals.Genetics, selection, evolution : GSE · 2016Article
- Identification of Beef Heifers with Superior Uterine Capacity for Pregnancy.Biology of reproduction · 2016Article
- Global assessment of imprinted gene expression in the bovine conceptus by next generation sequencing.Epigenetics · 2016Article
- Identification of Known and Novel Recurrent Viral Sequences in Data from Multiple Patients and Multiple Cancers.Viruses · 2016Article
- Article
- Use of Genomic Tools to Improve Cattle Health in the Context of Infectious Diseases.Frontiers in genetics · 2016Review
Corrections and comments
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Authors and funding
10 authors at 5 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundNext-generation sequencing projects commonly commence by aligning reads to a reference genome assembly. While improvements in alignment algorithms and computational hardware have greatly enhanced the efficiency and accuracy of alignments, a significant percentage of reads often remain unmapped.
resultsWe generated de novo assemblies of unmapped reads from the DNA and RNA sequencing of the Bos taurus reference individual and identified the closest matching sequence to each contig by alignment to the NCBI non-redundant nucleotide database using BLAST. As expected, many of these contigs represent vertebrate sequence that is absent, incomplete, or misassembled in the UMD3.1 reference assembly. However, numerous additional contigs represent invertebrate species. Most prominent were several species of Spirurid nematodes and a blood-borne parasite, Babesia bigemina. These species are either not present in the US or are not known to infect taurine cattle and the reference animal appears to have been host to unsequenced sister species.
conclusionsWe demonstrate the importance of exploring unmapped reads to ascertain sequences that are either absent or misassembled in the reference assembly and for detecting sequences indicative of parasitic or commensal organisms.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.