Where to get publicly available RNA-Seq data

If you want to practice these skills using a publicly available dataset or if you read a paper and want to download their data for your own analysis, here are some tips on how to do that.

If you want to start with gene counts:

Gene Expression Omnibus: Genomics data repository, typically with sequencing based and array based data. Search for study of interest (look for GSE ids in publication) or search for topic of interest. Go down to supplementary data and download counts file. Also, download the series matrix which has the sample metadata as well as sample processing details.

If you want to start with raw sequencing data:

Sequencing read archive: Look for SRR ids in your publication or search for topic of interest. You will need to use SRA-toolkit (available on TACC) to download fastq files corresponding to a particular study.

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