Response to 'comment on rigorous benchmarking of T cell receptor repertoire profiling methods for cancer RNA sequencing' by Davydov A.N.; Bolotin D.A.; Poslavsky S. V. and Chudakov D.M.
Response to 'comment on rigorous benchmarking of T cell receptor repertoire profiling methods for cancer RNA sequencing' by Davydov A.N.; Bolotin D.A.; Poslavsky S. V. and Chudakov D.M.
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对davydov A.N.的T细胞受体库库分析方法的严格基准测试方法的评论的回应； Bolotin D.A。； Poslavsky S. V.和Chudakov D.M.
DOI：
10.1093/bib/bbad355
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发表时间：
2023-09-22
影响因子：
9.5
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中科院分区：
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Huang等人的研究成果。答复：Davydov等人。讨论出版《癌症RNA测序中T细胞受体谱系分析方法的严格基准》中的潜在陷阱。下面，我们澄清并表明，不能根据他们的答复得出结论。Davydov等人。强调指出，我们在分析中不考虑Phred核苷酸质量的CATT、TRUST4和ImRep等工具与MiXCR的比较没有完全标准化。他们建议，为了确保公平的比较，MiXCR中的质量过滤器也应该禁用。我们感谢Davydov等人的宝贵建议。关于在执行MIXCR之前对读数实施Phred核苷酸质量过滤器的工作组。然而，我们在这本出版物中的主要目标是忠实地复制科学研究人员在利用计算工具时使用的典型工作流程。因此，在将各种生物信息学工具应用于同一组样本时，省略默认命令是不公平的。因此，我们选择在所有工具中使用统一的默认标准，以其默认设置执行每个工具。明确了1.0版中与克隆类型丰度计算相关的一个具体问题。TRUST4的2。我们当然赞赏Davydov等人提出的关切。关于1.0版中的一个潜在错误的小组。2可能会影响克隆丰度计算。保持最高标准的数据完整性至关重要，我们认真对待这类观察。然而，重要的是要注意，我们研究中使用的TRUST4版本是我们准备和进行分析以供发表时可用的版本。因此，我们的方法符合当时的最佳做法。Davydov等人。指出我们对免疫谱系提取工具的评估仅侧重于定量指标，
Huang et al. reply: Davydov et al. discuss potential pitfalls in the publication ‘Rigorous benchmarking of T cell receptor repertoire profiling methods for cancer RNA sequencing’. Below, we clarified and demonstrated that conclusions cannot be drawn on the basis of their response. Davydov et al. highlighted that our comparison of tools like CATT, TRUST4, and ImRep—which do not consider Phred nucleotide quality in their analyses—against MiXCR was not fully standardized. They suggested that to ensure a fair comparison, the quality filter in MiXCR should also be disabled. We acknowledge the valuable suggestion from the Davydov et al. group regarding the implementation of Phred nucleotide quality filters on the reads before executing MIXCR. However, our primary objective in this publication is to faithfully replicate the typical workflow employed by scientific researchers when utilizing computational tools. Consequently, it would be inequitable to omit the default command when applying various bioinformatics tools to the identical set of samples. Consequently, we opted to employ uniform default criteria across all tools, executing each tool with its default settings.Furthermore, Davydov et al. pinpointed a specific issue related to clonotype abundance calculation in version 1.0. 2 of TRUST4. We certainly appreciate the concerns raised by the Davydov et al. group regarding a potential bug in version 1.0. 2 of TRUST4 that might affect clonotype abundance calculations. It’s crucial to maintain the highest standards of data integrity, and we take such observations seriously. However, it’s important to note that the version of TRUST4 used in our study was the version available at the time we were preparing and conducting our analyses for publication. Therefore, our methodology was in accordance with best practices available at that time. Davydov et al. pointed out that our evaluation of immune repertoire extraction tools focused solely on quantitative metrics,