RNA velocity | RNA速率

单细胞转录组确实是利器，但我们大多只利用了表达的信息，而从reads到表达之间的信息完全被我们忽略了。

最近nature发了一篇单细胞方法类文章，讲得就是如何利用RNA velocity来做细胞发育路径的推断。

velocyto

velocyto-notebooks

RNA velocity of single cells

 

首先需要了解一些基本概念：

RNA velocity：the time derivative of the gene expression state—can be directly estimated by distinguishing between unspliced and spliced mRNAs in common single-cell RNA sequencing protocols. a high-dimensional vector that predicts the future state of individual cells on a timescale of hours. 比较抽象，一开始很难理解。

half-life of mRNA：Translation in both prokaryotes and eukaryotes involves three phases: initiation, elongation, and termination. The relative abundance of nascent (unspliced) and mature (spliced) mRNA can be exploited to estimate the rates of gene splicing and degradation. could reveal the rate and direction of change of the entire transcriptome during dynamic processes.

 

装R版本的时候，HDF5老是出问题，必须安装指定版本。同时还有一系列的预选包必须安装。

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1	brew switch hdf5 1.10.1_2

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1	conda install llvm

 

python版本也有问题：

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1	clang: error: unsupported option '-fopenmp'

 

If not, try conda install llvm, conda install gcc or conda install libgcc.
If this also does not work, try adding -c conda-forge I am pretty sure the version of the compiler provided by conda forge supports openmp.

 

for pagoda2

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cd /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ rm clang++ ln -s /usr/local/clang4/bin/clang++ clang++

　　

 合并

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1	ls results/*/*.loom |  sed "s:^:`pwd`/: " > loom.file.list

　　

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import loompy   files = []   inf = open("loom.file.list", "r") for line in inf:     files.append(line.strip()) inf.close()   loompy.combine(files, "merged.loom", key="Accession")

　　

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import velocyto as vcy vlm = vcy.VelocytoLoom("merged.loom") vlm.ca len(dir(vlm))

　　

 

这里有个PPT，总结了该工具的基本算法。RNA_velocity.pptx

另外有一个叫velocyto可以分析。示例分析：RNA velocity analysis.pptx

　　

　　

针对velocyto会再开一个简易教程。

 

参考：

What happens to the mRNA after it has completed its job at the ribosome and the protein has been released?

Database for mRNA Half-Life of 19 977 Genes Obtained by DNA Microarray Analysis of Pluripotent and Differentiating Mouse Embryonic Stem Cells 

Messenger RNA Half-Life Measurements in Mammalian Cells