zUMIs - A fast and flexible pipeline to process RNA sequencing data with UMIs.
zUMIs - A fast and flexible pipeline to process RNA sequencing data with UMIs.
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DOI：
10.1093/gigascience/giy059
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发表时间：
2018-06-01
期刊：
影响因子：
9.2
通讯作者：
Hellmann I
中科院分区：
文献类型：
--
作者：
Parekh S;Ziegenhain C;Vieth B;Enard W;Hellmann I
单细胞RNA测序（scRNA-seq）实验通常在扩增cDNA后分析数百或数千个细胞。通过早期引入样品特异性条形码（BC）实现了高通量，并且通过独特的分子标识符（UMI）减轻了扩增偏倚。因此，scRNA-seq数据的理想分析管道需要根据BC和UMI两者有效地将读数制表。 zUMI是一个流水线，可以处理已知和随机BC，也可以有效地折叠UMI，无论是仅用于外显子映射读取还是用于外显子和内含子映射读取。如果BC注释缺失，则zUMI可以从测序读数的分布中准确地检测完整细胞。zUMI的另一个独特功能是自适应下采样功能，该功能有助于处理差异巨大的文库大小，但也允许用户评估文库是否已被测序至饱和。为了说明zUMI的实用性，我们分析了单核RNA-seq数据集，并显示超过35%的读取映射到内含子。此外，我们表明，这些内含子读段是关于表达水平的信息，显着增加了检测到的基因的数量，并提高了聚类分辨率。 zUMI的灵活性使得可以容纳使用BC和UMI的任何主要scRNA-seq协议生成的数据，并且是处理此类scRNA-seq数据的功能最丰富，快速和用户友好的管道。
Single-cell RNA-sequencing (scRNA-seq) experiments typically analyze hundreds or thousands of cells after amplification of the cDNA. The high throughput is made possible by the early introduction of sample-specific bar codes (BCs), and the amplification bias is alleviated by unique molecular identifiers (UMIs). Thus, the ideal analysis pipeline for scRNA-seq data needs to efficiently tabulate reads according to both BC and UMI. zUMIs is a pipeline that can handle both known and random BCs and also efficiently collapse UMIs, either just for exon mapping reads or for both exon and intron mapping reads. If BC annotation is missing, zUMIs can accurately detect intact cells from the distribution of sequencing reads. Another unique feature of zUMIs is the adaptive downsampling function that facilitates dealing with hugely varying library sizes but also allows the user to evaluate whether the library has been sequenced to saturation. To illustrate the utility of zUMIs, we analyzed a single-nucleus RNA-seq dataset and show that more than 35% of all reads map to introns. Also, we show that these intronic reads are informative about expression levels, significantly increasing the number of detected genes and improving the cluster resolution. zUMIs flexibility makes if possible to accommodate data generated with any of the major scRNA-seq protocols that use BCs and UMIs and is the most feature-rich, fast, and user-friendly pipeline to process such scRNA-seq data.
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DOI：
10.1126/science.1247651
发表时间：
2014-02-14
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Jaitin DA;Kenigsberg E;Keren-Shaul H;Elefant N;Paul F;Zaretsky I;Mildner A;Cohen N;Jung S;Tanay A;Amit I
通讯作者：
Amit I
影响因子：
46.9
作者：
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通讯作者：
Stadler, Michael B.
影响因子：
48
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Habib N;Avraham-Davidi I;Basu A;Burks T;Shekhar K;Hofree M;Choudhury SR;Aguet F;Gelfand E;Ardlie K;Weitz DA;Rozenblatt-Rosen O;Zhang F;Regev A
通讯作者：
Regev A
影响因子：
7.7
作者：
Regev, Aviv;Teichmann, Sarah A;Yosef, Nir
通讯作者：
Yosef, Nir
影响因子：
12.3
作者：
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通讯作者：
Smyth GK