Doc_ID: A08-0001GRCm38en101Star275a

Editor: Mira

Reviewer : Anita

Description

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.

Build RSEM references using RefSeq, Ensembl, or GENCODE annotations
RefSeq and Ensembl are two frequently used annotations. For human and mouse, GENCODE annotaions are also available. In this, we show how to build RSEM references using Ensembl annotation. Note that it is important to pair the genome with the annotation file for each annotation source. 

Source

Download

• URL:
  1. DNA Sequrnce：ftp://ftp.ensembl.org/pub/release-101/fasta/mus_musculus/dna/=>點選”Mus_musculus.GRCm38.dna.primary_assembly.fa.gz”，進行下載
  2. GTF：ftp://ftp.ensembl.org/pub/release-101/gtf/mus_musculus/=>點選”Mus_musculus.GRCm38.101.chr.gtf.gz”，進行下載

File size : 1. Mus_musculus.GRCm38.dna.primary_assembly.fa.gz 769MB (解壓縮後2.71GB)

                2. Mus_musculus.GRCh38.101.chr.gtf.gz 31.9MB (解壓縮後1.01GB)

Genome assemble version:GRCm38 Release 101

Detail information:
使用STAR version 2.7.5a及RSEM version 1.3.3 來製作index，請確認已完成GApp standard analysis environment的安裝

#Activate standard analysis environment

conda activate GApp

#移動到工作區(依user設定的工作區而定)

cd /User_Work

#創建放置fasta及GTF的資料夾
mkdir -p refs/Mus_musculus/GRCm38en101Star2.7.5a/

#移動至資料夾

cd refs/Mus_musculus/GRCm38en101Star2.7.5a/

#下載fasta
wget ftp://ftp.ensembl.org/pub/release-101/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.primary_assembly.fa.gz

#解壓縮檔案
gunzip  Mus_musculus.GRCm38.dna.primary_assembly.fa.gz

#下載GTF
wget ftp://ftp.ensembl.org/pub/release-101/gtf/mus_musculus/Mus_musculus.GRCm38.101.chr.gtf.gz
 

#解壓縮檔案
gunzip Mus_musculus.GRCm38.101.chr.gtf.gz

#用RSEM及STAR prepare index

rsem-prepare-reference \
–gtf /User_Work/refs/Mus_musculus/GRCm38en101Star2.7.5a/Mus_musculus.GRCm38.101.chr.gtf \
–star \
-p 20 \
/User_Work/refs/Mus_musculus/GRCm38en101Star2.7.5a/Mus_musculus.GRCm38.dna.primary_assembly.fa\
/User_Work/refs/Mus_musculus/GRCm38en101Star2.7.5a/GRCm38.101.genome

Statistics

Summary

Gene counts (Primary assembly)

Gene counts (Alternative sequence)

Other

Index and modification

Index

Bundle files