How can I get test data (raw count) for my algorithm?

Question

[ghmdsr]

Hi

I'm first year graduate student.

I make an algorithm, so I want to test my algorithm ... but i don't know where I can get it.

Input data for my algorithm is transcriptome data. I need raw count data, (especially, about kinase amplification)

Please let me know where I can get raw count data.

[cpad0112]

if you know the data (format) structure accepted by algorithm, you can simulate data in statistical languages (R etc) or you can use existing R packages such as SimSeq

Answer 1

[Kevin Blighe]

Search the main sequence repositories:

• European Nucleotide Archive
• Sequence Read Archive
• ArrayExpress
• Gene Expression Omnibus

In most cases, you will be able to download raw FASTQ reads, aligned BAMs, and / or the raw count data.

Kevin

Answer 2

[Friederike]

sounds like a great use-case for the recount2 package -- it provides expression data for genes, exons, exon–exon splice junctions and base-level coverage and it is absolutely meant for downloading and software testing (Reference, vignette)

The big plus is that the data was processed in a fairly standardized, transparent way.