Alignment

Overview

Using STAR to get the bam file of each sample. Meanwhile, in order to facilitate the subsequent analysis, we sort the bam with samtools.

Prerequisites

Java 8
http://www.oracle.com/technetwork/java/javase/overview/java8-2100321.html

Samtools
http://samtools.sourceforge.net/

Usage

From command line,

• java -Xmx100g -jar SiPAS-tools.jar -a Alignment -f ./Alignment_parameter.txt > log.txt &

The content of the parameter file is as follows.

@App:	Alignment
@Author: Jun Xu
@Email: junxu1048@genetics.ac.cn
#The directory of input.
/data2/junxu/SiPAS-tools/30_1/
#Mode of alignment. PE or SE. The default is PE mode
PE
#Number of loci of multiple alignment. If the value is 10, it means that a read mapping to more than 10 position will be discarded. The default is 2
10
#The rate of mismatch. If this value is greater than set value, this read will be discard. The defult is 0.1
0.1
#The minimun number of match
80
#The minimun reads number of each library. The default value is 1M reads.
0
#The threads used for run this pipeline. The default value is 32.
32
#Index position of STAT. If it is empty, it will generate starLib filr in the output directory.
/data2/junxu/starLib1.1
#The gene annotation file (GTF format)
/data1/home/junxu/*.gtf
#The gene reference file (fa format)
/data1/home/junxu/*.fa
#The path of STAR alignment software
/data1/home/junxu/software/STAR-2.6.1c/bin/Linux_x86_64/STAR

The file is available here.

Author

Jun Xu
https://github.com/Junjun-Xu

Xiaohan Yang
https://github.com/Yangxiaohan0120

Song Xu
https://github.com/XscapeCn

Fei Lu
flu@genetics.ac.cn; dr.lufei@gmail.com
https://github.com/Fei-Lu