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Non-referenced genome assembly from epigenomic short-read data
journal contribution
posted on 2014-01-01, 00:00 authored by A Kaspi, Mark ZiemannMark Ziemann, S T Keating, I Khurana, Timothy ConnorTimothy Connor, Briana RandallBriana Randall, Adrian Cooper, R Lazarus, Ken WalderKen Walder, P Zimmet, A El-OstaCurrent computational methods used to analyze changes in DNA methylation and chromatin modification rely on sequenced genomes. Here we describe a pipeline for the detection of these changes from short-read sequence data that does not require a reference genome. Open source software packages were used for sequence assembly, alignment, and measurement of differential enrichment. The method was evaluated by comparing results with reference-based results showing a strong correlation between chromatin modification and gene expression. We then used our de novo sequence assembly to build the DNA methylation profile for the non-referenced Psammomys obesus genome. The pipeline described uses open source software for fast annotation and visualization of unreferenced genomic regions from short-read data.
History
Journal
EpigeneticsVolume
9Issue
10Pagination
1329 - 1338Publisher DOI
ISSN
1559-2294eISSN
1559-2308Publication classification
C Journal article; C1 Refereed article in a scholarly journalCopyright notice
2014, Taylor & FrancisUsage metrics
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Keywords
Science & TechnologyLife Sciences & BiomedicineBiochemistry & Molecular BiologyGenetics & HeredityChIP-seqDNA methylationde novo assemblyepigenomic integrationHigh-throughput sequencingMBD-seqPsammomys obesusINTRAUTERINE GROWTH-RETARDATIONGENETIC-VARIATIONPSAMMOMYS-OBESUSSAND RATSEQ DATAIDENTIFICATIONEXPOSUREFAMINEALIGNMENTChIP-seq, immunoprecipitated chromatin sequencingDMR, differentially methylated regionMBD-seq, methyl binding domain protein sequencingMeDIP-seq; methylated DNA immunoprecipitation sequencingRNA-seq, RNA sequencingGenetics
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