PASA的安装与使用

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所属分类:Bioinformatics

1. PASA简介

PASA, acronym for Program to Assemble Spliced Alignments, is a eukaryotic genome annotation tool that exploits spliced alignments of expressed transcript sequences to automatically model gene structures, and to maintain gene structure annotation consistent with the most recently available experimental sequence data. PASA also identifies and classifies all splicing variations supported by the transcript alignments.

Note:
Combine genome and Trinity de novo RNA-Seq assemblies to generate a comprehensive transcript database.

2. PASA使用前的准备

2.1 Mysql数据库的准备

创建只读权限用户和所有权限用户各一个。

2.1 安装perl模块

2.3 安装GMAP

2.4 安装BLAT

2.5 安装FASTA

2.6 安装PASA

2.7 安装GD

安装GD需要先行安装libgd

再安装GD

安装GD的目的是能通过网页来查看PASA的运行结果。

2.8 配置PASA

2.8.1. 修改PASA的配置文件$PASAHOME/pasa_conf/conf.txt

2.8.2. 该文件需要修改的地方:

2.8.3. 修改httpd配置文件,

在/etc/httpd/conf/httpd.conf添加如下几行:

2.9 cleaning the transcript sequences[Optional, requires seqclean to be installed

下载两个污染数据库,为fasta文件。

UniVec_Core includes only oligonucleotides and vectors consisting of bacterial, phage, viral, yeast or synthetic sequences. Vectors that include sequences of mammalian origin are excluded.

3. PASA主程序的使用

PASA的主程序是: $PASAHOME/scripts/Launch_PASA_pipeline.pl, 其使用参数如下:

原文来自:http://www.chenlianfu.com/?p=1133

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