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

Bioinformatics Coach
Bioinformatics Coach
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 Support this Channel ________________________________________________________________________________________________ https://www.buymeacoffee.com/informatician https://paypal.me/theinformatician Support me on Patreon ________________________________________________________________________________________________ https://www.patreon.com/bigdataanalytics Subscribe to my channels ________________________________________________________________________________________________ Bioinformatics: https://www.seevid.ir/fa/result?ytch=UCOJM9xzqDc6-43j2x_vXqCQ Data Science: https://www.seevid.ir/fa/result?ytch=UC3bjbWYK7S_FLW0y0Ux4tyQ Short Clips: https://www.seevid.ir/fa/result?ytch=UCrJE3zmKNdkmPsh_6TIPIIg How to Install Anaconda ________________________________________________________________________________________________ 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 ________________________________________________________________________________________________ https://github.com/vappiah/Transcriptomics/tree/main/Tutorials/gene-expression-analysis/Episode-1 Download data ________________________________________________________________________________________________ ftp://ftp.ccb.jhu.edu/pub/RNAseq_protocol/chrX_data.tar.gz Video Chapters ________________________________________________________________________________________________ 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 ________________________________________________________________________________________________ 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 ________________________________________________________________________________________________ https://clarity.fm/vincentappiah Reach out [email protected] #bioinformatics #datascience #datasciencecourse #datasciencetutorial #linux #rnaseq #rprogramming gene expression,gene expression analysis,rna sequencing,rna seq,rna seq data analysis,rna seq analysis,rna seq data analysis using r,rna sequencing data analysis,rna sequencing explained,rna sequencing illumina,rna sequencing data analysis tutorial,rna seq galaxy,rna seq analysis tutorial r,rna seq normalization,deseq2,edgeR,bioinformatics,bioinformatics python,bioinformatics day in the life,bioinformatics coach,bioinformatics course
2 سال پیش در تاریخ 1401/01/26 منتشر شده است.
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