Isoform-level ribosome occupancy estimation guided by transcript abundance with Ribomap
Isoform-level ribosome occupancy estimation guided by transcript abundance with Ribomap
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DOI：
10.1093/bioinformatics/btw085
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发表时间：
2016-06-15
期刊：
影响因子：
5.8
通讯作者：
Kingsford, Carl
中科院分区：
文献类型：
--
作者：
Wang, Hao;McManus, Joel;Kingsford, Carl
摘要：核糖体分析是一项最近开发的高通量测序技术，可在翻译过程中捕获约 30 bp 长的核糖体保护的 mRNA 片段。由于选择性剪接和重复序列，核糖体保护的读段可能映射到转录组中的许多位置，从而在使用标准方法时导致丢弃或任意映射。我们提出了一种技术和软件，通过将读数分配给与估计的转录本丰度成比例的潜在起源来解决这个问题。与简单的映射相比，这可以更准确地估计核糖体谱。
The Summary: Ribosome profiling is a recently developed high-throughput sequencing technique that captures approximately 30 bp long ribosome-protected mRNA fragments during translation. Because of alternative splicing and repetitive sequences, a ribosome-protected read may map to many places in the transcriptome, leading to discarded or arbitrary mappings when standard approaches are used. We present a technique and software that addresses this problem by assigning reads to potential origins proportional to estimated transcript abundance. This yields a more accurate estimate of ribosome profiles compared with a naive mapping.