RNA seq data analysis
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15 months ago

I need films to teach me the steps of RNA seq data analysis I dont know how I can download the data from SRA bank in NCBI please help me

RNA seq data analysis • 526 views
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It is usually easier to download the data deposited in the SRA via either GEO or ENA

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thank you very much but I just can download the data from SRA!!!

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It seems like you have been tasked to do something for which you have no experience. This reflects poorly on your supervisor (if you have one). Biostars should not be a substitute for one's own supervisor.

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yes thats right , I dont have any experience about this subjec

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No problem - one always has to start somewhere. Try the suggestions of my colleagues. From the other thread, Galaxy is also a good place to start.

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I'm confused. You know or you do not know how to download data from SRA?

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Follow the comprehensive RNAseq tutorial from Griffith lab: https://github.com/griffithlab/rnaseq_tutorial

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15 months ago
dsull ★ 2.3k

Let's start with something basic:

Use BioJupies to analyze your data: https://amp.pharm.mssm.edu/biojupies/

Search for your dataset, assign samples to groups, and then you can analyze everything with just a few mouse clicks.

Once you get familiar with the basics of RNAseq, then download the raw FASTQ files and analyze it yourself. Until then, stick with tools that do everything for you and that have a nice user-friendly interface.

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15 months ago
GenoMax 107k

If you learn visually then here is one set of tutorials. Look at the link in description to download example data/slides etc. There are many other tutorials available on YouTube. Quality is going to vary so decide for yourself.

Once you are ready to download other RNAseq data use sra-explorer: C: sra-explorer : find SRA and FastQ download URLs in a couple of clicks

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15 months ago

I recently recorded a video for students covering the very basic steps for dif. expression analysis using RNA-Seq, though it does not cover data fetching from databases.

Hope it helps to grasp the basics

https://www.loom.com/share/a55c1dedb8e64e7cac47f6595b751de7

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15 months ago
Barry Digby ▴ 780

This video should be what you want:

#16 Lockdown Learning Bioinformatics-along: Downloading from the SRA

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