README.md

In liutao199527/scAPAtrap1: scAPAtrap

scAPAtrap

Introduction

Alternative polyadenylation (APA) has been indicated to play an important role in regulating mRNA stability, translation and localization. Diverse scRNA-seq protocols, such as Drop-seq, CEL-seq, and 10x Genomics, utilizing 3′ selection/enrichment in library construction, provides opportunities to extend bioinformatic analysis for studying APA at single cell resolution. We proposed a tool called scAPAtrap for identification and quantification of APA sites in each individual cells by leveraging the resolution and huge abundance of scRNA-seq data generated by various 3’ tag-based protocols. scAPAtrap incorporates peak identification and poly(A) read anchoring, which is capable of identifying precise locations of APA sites and sites even with low read coverage. scAPAtrap can also quantify the expression levels of all identified APA sites, considering duplicates resulted from both IVT and PCR cycles.

Prerequisites

Tools

• samtools
• subread
• umi_tools
• star
• R version 3.5.3, or above.

以上工具的安装，可以利用conda进行安装

conda install samtools -c bioconda
conda install subread -c bioconda
conda install umi_tools -c bioconda
conda install star -c bioconda

R packages

Please install the R packages as follow: GenomicRanges、GenomicAliments、dplyr、derfinder、regionR、devtools

data

文章中主要用到的三个数据： mouse_speram(GSE104556) plant_TIAR([]) * Grun()

帮助文档中所需要的数据，请访问这个链接进行下载。

Installing

install.packages('devtools') devtools::install_github("BMILAB/scAPAtrap")

Application examples

Identified and Quantify polyAsite

In this case study, we investigated the application of scAPAtrap on demo.bam from 3’ end sequencing. Please refer to the vignette (HTML) for full details.

## You can also browse the vignette using the following command on the R console
browseVignettes('scAPAtrap')

Downstream Analysis

In this case,我们将复现论文中speram数据三个方法比较的结果，和speram数据scAPAtrap方法DE分析的结果，你可以访问这个链接，下载到代码中所需要的全部数据。代码实现过程请参考[scAPAtrap_compare.html]和[scAPAtrap_DE.html]

Citation

If you are using scAPAtrap, please cite: Tao Liu,Wenbin Ye, Congting Ye, and Xiaohui Wu: scAPAtrap: Modeling and visualization of dynamics of alternative polyadenylation across biological samples (under review).

liutao199527/scAPAtrap1 documentation built on Aug. 16, 2020, 7:24 p.m.