Using NCBI GEO to obtain raw and count data for RNA-seq

doi.org/10.7875/togotv.2023.075
NCBI GEO (Gene Expression Omnibus) is a database of gene expression information provided and maintained by NCBI. Not only can you search for expression data sets and gene profiles of your interest among them, but also you can freely download the raw data.
In this video, we will show you how to download the data necessary for RNA-seq analysis using the Mac terminal and how to create a fastq file. The first half of the video explains how to build an environment using Homebrew as a necessary preparation before downloading the data. The second half explains how to download multiple RNA-seq data in parallel using the SRA Toolkit and pigz, and how to compress and save the data.
0:00 Using NCBI GEO to obtain raw RNA-seq data and count data
00:09 1. installing Homebrew
01:10 2. installation of SRA Toolkit
02:01 3. installation of Pigz
02:30 4. creation of directories
03:18 5. downloading RNA-seq data
04:36 6. downloading multiple RNA-seq data
06:28 7. converting to fastq files
07:28 8. converting multiple files to fastq
08:16 9. compressing fastq files with pigz
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