How I analyze RNA Seq data using HISAT2 , SAMTOOLS , STRINGTIE BALLGOWN & R
18.6 هزار بار بازدید -
2 سال پیش
-
This video shows you how
This video shows you how to analyse rna seq data.
Map with hisat2
quantify genes with stringtie
Identify deferentially expressed genes using ballgown
Visualize data using R
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How to Install Anaconda
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Linux https://www.seevid.ir/fa/w/AshsPB3KT-E
MacOS https://www.seevid.ir/fa/w/Obl6oyh5S58 - GUI Installer
https://www.seevid.ir/fa/w/HdQoR5QqjoY - Command line installer
Get the master script from my github repo
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https://github.com/vappiah/Transcriptomics/tree/main/Tutorials/gene-expression-analysis/Episode-1
Download data
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ftp://ftp.ccb.jhu.edu/pub/RNAseq_protocol/chrX_data.tar.gz
Video Chapters
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https://www.seevid.ir/fa/w/CAa1g6-3Szc intro and PC Requirement
https://www.seevid.ir/fa/w/CAa1g6-3Szc setting up the analysis environment
https://www.seevid.ir/fa/w/CAa1g6-3Szc download example data
https://www.seevid.ir/fa/w/CAa1g6-3Szc indexing
https://www.seevid.ir/fa/w/CAa1g6-3Szc mapping
https://www.seevid.ir/fa/w/CAa1g6-3Szc sorting mapped reads
https://www.seevid.ir/fa/w/CAa1g6-3Szc transcript assembly
https://www.seevid.ir/fa/w/CAa1g6-3Szc estimate abundance
https://www.seevid.ir/fa/w/CAa1g6-3Szc identify differentially expressed genes and transcripts
https://www.seevid.ir/fa/w/CAa1g6-3Szc data visualization
https://www.seevid.ir/fa/w/CAa1g6-3Szc explore output files
https://www.seevid.ir/fa/w/CAa1g6-3Szc result interpretation
Reference
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https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5032908/pdf/nihms816842.pdf
https://github.com/bioinformatics-ca/CAN_2021/blob/main/Module6/module6lab_Rnotebook.html
https://davetang.org/muse/2017/10/25/getting-started-hisat-stringtie-ballgown/
https://bioinformaticsdotca.github.io/CAN_2021
https://pydupont.github.io/BallGownTuto/Protocol.html
https://biocorecrg.github.io/CRG_RIntroduction/volcano-plots.html
https://github.com/bioinformatics-ca/CAN_2021/blob/main/Module6/module6lab_Rnotebook.html
Book a Session
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2 سال پیش
در تاریخ 1401/01/26 منتشر شده
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