文章基本信息

标题：Reply to Iñiguez et al.: ERVmap is a validated approach to mapping proviral endogenous retroviruses in the human genome
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作者：Adam Karczmarz ; Jakub Lacki ; Adam Karczmarz 等
期刊名称：Proceedings of the National Academy of Sciences
印刷版ISSN：0027-8424
电子版ISSN：1091-6490
出版年度：2019
卷号：116
期号：43
页码：21352-21353
DOI：10.1073/pnas.1908504116
出版社：The National Academy of Sciences of the United States of America
摘要：Iñiquez et al. (1) claim that ERVmap (2) contains methodological errors and Telescope is more accurate in assigning ambiguous reads (1, 3). Telescope detected 19 elevated and 4 repressed endogenous retroviruses (ERVs), while ERVmap found 124 elevated ERVs (2). Iñiquez et al. (1) claim that this difference is due to methodological flaws in our read alignment, ERV annotation, and failure to account for sequencing platform variance. We disagree with all 3 points for the following reasons. ERVmap identifies a best read match through stringent filtering criteria put forth by experts (4, 5). In the absence of a gold standard to call multimapped reads, we intentionally over-discard to avoid miscalling.