For heatmap generation, how to retrieve required data from SRA dataset?
The SRA contains raw sequencing reads, which require multiple steps for gene expression analysis. First, the raw data must be downloaded and preprocessed by trimming adapters and conducting quality control. Then, the preprocessed reads are mapped to a reference genome, followed by output format conversion and reads count matrix generation. Finally, the generated matrix is used for gene expression analysis.
If you only care about normalized data to make a heatmap, you can use recount3. NCBI itself is also starting to offer raw and normalized RNA-Seq counts (beta version). You can also take a look at GEOexplorer Article recount3: summaries and queries for large-scale RNA-seq expr...
https://www.ncbi.nlm.nih.gov/geo/info/rnaseqcounts.html
https://www.ncbi.nlm.nih.gov/geo/info/geo2r.html
https://academic.oup.com/nar/article/50/W1/W367/6591531
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