How I analyze RNA Seq data using HISAT2 , SAMTOOLS , STRINGTIE BALLGOWN & R

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    • Install , Configure and Run Anaconda in  a...  
MacOS    • How to Install and Run Anaconda in  MacOS ...   - GUI Installer
   • Install, Configure and Run Anaconda in ANY...   - Command line installer

Get the master script from my github repo
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https://github.com/vappiah/Transcript...

Download data
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ftp://ftp.ccb.jhu.edu/pub/RNAseq_protocol/chrX_data.tar.gz


Video Chapters
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00:00 intro and PC Requirement
01:08 setting up the analysis environment
12:31 download example data
20:24 indexing
26:22 mapping
29:08 sorting mapped reads
32:01 transcript assembly
45:34 estimate abundance
47:14 identify differentially expressed genes and transcripts
01:48:03 data visualization
01:50:04 explore output files
01:55:44 result interpretation

Reference
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https://www.ncbi.nlm.nih.gov/pmc/arti...
https://github.com/bioinformatics-ca/...
https://davetang.org/muse/2017/10/25/...
https://bioinformaticsdotca.github.io...
https://pydupont.github.io/BallGownTu...
https://biocorecrg.github.io/CRG_RInt...
https://github.com/bioinformatics-ca/...


Book a Session
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https://clarity.fm/vincentappiah
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