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Open Tumor / Normal pair dataset for benchmarking and training

splaisansplaisan Leuven (Belgium)Member ✭✭

I am looking for a real tumor normal pair dataset to apply analysis and compare callers. Do you know of one I can get (bam would be quicker but even fastq is OK as I could map against 38 to be up-to-date).
I only found the Texas open data for which I would need to fill a consent which will be an issue when I use that data in training. I would prefer a fully open dataset and do not like the idea of working with two 1000g samples and pretend one is the tumor of the second (maybe good enough for developing software but I want to look at the data and make sense out of it).

Best Answers

  • splaisansplaisan Leuven (Belgium) ✭✭
    Accepted Answer

    Thanks Sheila,
    Actually I needed a full genome size sample as this will be used to evaluate both computing time and global genome metrics.
    I found exome-seq datasets for cancer and normal (SRA045832_cancer-exome) and did with that. Not exactly what i wanted but of reduced size and still showing all genes.
    Thanks for your help


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