6.RNA Regulation Analyses

0) Table of Contents

Target
Sequencing Methods
Bioinformatics Tools
Abundance
RNA-seq
DEGseq2, EdgeR, Cufflinks
Splicing
RNA-seq
rMATs, TOPHAT/Cufflinks
Editing
RNA-seq
GIREMI, REDItools, SPRINT
APA (Alternative Ploy-adenylation)
RNA-seq/PAT-seq
DaPars, APAtrap
Translation
Ribo-seq
RiboWave, RiboTaper, ORFscore
Degradation
Degradome-Seq (PARE-seq)
sPARTA
Modification
m6A-seq, MeRIP-seq, miCLIP
m6aViewer, MeRIP-PF
Structure
icSHAPE, SHAPE-map, DMS-seq
RNAstructure, RNAfold, RME
RNA-protein interaction
HITS-CLIP, PAR-CLIP, iCLIP, eCLIP
Piranha, PARalyzer, CIMS; POSTAR/CLIPdb

1) Files Needed

Method 1: Use Docker

docker images的下载链接如附表所示:
(1) 6.1 Alternative Splicing: bioinfo_PartI-PartII-PartIII1-3.tar.gz
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#与PART I + II类似
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docker load -i ~/Desktop/bioinfo_PartI-PartII-PartIII1-3.tar.gz #load the image
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docker run --name=bioinfo_tsinghua -dt -h bioinfo_docker --restart unless-stopped -v ~/Desktop/bioinfo_tsinghua_share:/home/test/share xfliu1995/bioinfo_tsinghua:2
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docker exec -it rnaeditor bash
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cd /home/test/alter-spl/
Copied!
(2) 6.2 APA, 6.8 Ribo-seq, 6.9 Structure-seq:bioinfo_tsinghua_6.2_apa_6.3_ribo_6.4_structure.tar.gz
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docker load -i ~/Desktop/bioinfo_tsinghua_6.2_apa_6.3_ribo_6.4_structure.tar.gz
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#注意:下面的文件挂载目录为~/Desktop/bioinfo_tsinghua_share, 自己运行时记得改为自己新建的一个目录名称。
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docker run --name=rnaregulation -dt -h bioinfo_docker --restart unless-stopped -v ~/Desktop/bioinfo_tsinghua_share:/home/test/share gangxu/bioinfo_tsinghua_6.2_apa_6.3_ribo_6.4_structure:latest
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docker exec -u root -it rnaregulation bash
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# APA
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cd /home/test/rna_regulation/apa
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# Ribo-seq
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cd /home/test/rna_regulation/ribo-wave
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# Structure-seq
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cd /home/test/rna_regulation/structure_seq
Copied!
(3) 6.3.Chimeric RNA Detection: bioinfo_chimeric.tar.gz
需要下载原始数据和基因组文件ctat_genome_lib_build_X_docker.zip,ref_genome.fa.star.idx.zip,请把 ref_genome.fa.star.idx 移到 ctat_genome_lib_build_X_docker文件中。下载解压后需要挂载。
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docker load -i ~/Desktop/bioinfo_chimeric.tar.gz
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mv ~/Downloads/ref_genome.fa.star.idx ~/Downloads/ctat_genome_lib_build_X_docker
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docker run -dt -v ~/Downloads/ctat_genome_lib_build_X_docker:/data --name=bioinfo_starfusion gangxu/starfusion:latest
Copied!
(4) 6.4 RNA Editing: bioinfo_rnaeditor.1.8.tar.gz
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docker load -i ~/Desktop/bioinfo_rnaeditor.tar.gz
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#注意:下面的文件挂载目录为/Users/xugang/Downloads/data2, 自己运行时记得改为自己新建的一个目录名称。
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docker run --name=rnaeditor -dt -h bioinfo_docker --restart unless-stopped -v /Users/xugang/Downloads/data2:/data2 gangxu/rnaeditor:1.8
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docker exec -it rnaeditor bash
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cd /home/test
Copied!
(5) 6.6.SNV/INDEL Detection: bioinfo_snv.tar.gz
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docker load -i ~/Downloads/bioinfo_snv.tar.gz
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docker run -dt --name=snv -v ~/Downloads/data:/data gangxu/snv:2.0
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docker exec -it snv bash
Copied!
(6) 6.10.CLIP-seq: bioinfo_clip_seq.tar.gz
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docker import bioinfo_clip_seq.tar.gz zs/clip_seq_analysis_ta:v1
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docker run --name=clip_seq_v1 -t -d -h CLIP_docker --restart unless-stopped zs/clip_seq_analysis_ta:v1 /bin/bash
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docker exec -it clip_seq_v1 bash
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su CLIP_user;
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cd ~
Copied!

Method 2: Directly Download

    如果不使用docker,也可以直接从该链接Files needed by this Tutorial中的清华云Bioinformatics Tutorial / Files路径下的相应文件夹中下载所需要的文件。

3) Teaching Videos (link)

    PART III: RNA Regulation Analyses
Last modified 27d ago