DOC_ID : T15-0002

RNA_QUA module : 

DOC_ID : M31-3000
Editor : Anita
Reviewer : Angela

Function :

    RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data. The RSEM package provides an user-friendly interface, supports threads for parallel computation of the EM algorithm, single-end and paired-end read data, quality scores, variable-length reads and RSPD estimation. In addition, it provides posterior mean and 95% credibility interval estimates for expression levels. For visualization, It can generate BAM and Wiggle files in both transcript-coordinate and genomic-coordinate.

    There are many usages of RSEM, here we can use it to calculate Expression Values.To calculate expression values, module will run the rsem-calculate-expression program. In this module will set some parameters :

• -p/–num-threads : Number of threads to use. Both Bowtie/Bowtie2, expression estimation and ‘samtools sort’ will use this many threads.
• –paired-end : Input reads are paired-end reads.
• –bam : Input file is in BAM format.

In its default mode, this program aligns input reads against a reference transcriptome with Bowtie and calculates expression values using the alignments. RSEM assumes the data are single-end reads with quality scores, unless the ‘–paired-end’ or ‘–no-qualities’ options are specified. 

After executing the rsem-calculate-expression program, the file will be output : 

• sample_name.isoforms.results : File containing isoform level expression estimates. 
• sample_name.genes.results : File containing gene level expression estimates.
• sample_name.stat : This is a folder instead of a file. All model related statistics are stored in this folder. Use ‘rsem-plot-model’ can generate plots using this folder.
• sample_name.alleles.results : Only generated when the RSEM references are built with allele-specific transcripts.
• sample_name.transcript.bam, sample_name.transcript.sorted.bam and sample_name.transcript.sorted.bam.bai : Only generated when –no-bam-output is not specified.
• sample_name.time : Only generated when –time is specified.

Ref : http://deweylab.github.io/RSEM/README.html, http://deweylab.biostat.wisc.edu/rsem/rsem-calculate-expression.html

Installation :

All software are included in GA environment. 

Note :

►執行分析前請先利用CreateProject.sh創建一個專案資料夾，請參閱Project standard folder structure文件。

►執行模組需確認所屬計算節點(–partition) : 一般節點的使用者建議使用ct56 ; 生醫節點的使用者建議使用ngs48G^註1。

►欲了解模組使用的方式，請執行模組的 -h 指令
 

#註1 : 欲確認使用者身分，請登入國網中心iService後，選取會員中心/計畫管理/我的計畫，若計畫名稱為”國家生醫數位資料與分析運算雲端服務平台III”即為生醫節點使用者

Description :

Usage :

The following explains the usage of module parameters :