Where to Download Cancer Raw Reads (fastq)?

Question

[louis-gil]

Does anyone know where I can download cancer raw reads (fastq files), tumor and Germline for non-humans?

I wanted to make a study with human data but I don't have the control access to download raw reads.

[ATpoint]

Why not apply for them? Typically a PI does it on your behalf (so you write it, they sign it). Plenty of material then available from NCBI/ICGC/TCGA.

[finswimmer]

Hello louis-gil ,

please tell us when you cross-post your question. This question is also asked on stackexchange.

Thanks!

fin swimmer

Answer 1

[manuel.belmadani]

Search for them on GEO, which links you to where you can download them on SRA. In the GEO results, find the accession IDs you need (e.g. SRPxxxxx for an SRA Project), and then you can choose individual runs (SRRxxxxxx) that are relevant from the projects. Most should be available to download them from SRA with no special access ( e.g. you can download the .sra files and extract the reads using fastq-dump.)

Crude example search: Cancer tumor germline AND ("gse"[Filter] AND "Expression profiling by high throughput sequencing"[Filter])

Still, there seems to be a few relevant datasets. Open them up and see what makes sense. You can probably make the search more specific (e.g. specify which organism for germline instead of all the keyword in one go like I did.)