Cancer exome sequences

Question

[phoenix.sum13]

Hi, I'm a beginner in this field. I wish to download some cancer-related sequences to practice making Variant Calling Pipeline. Where can I find such sequences? Can you download such sequences from the SRA database??

Answer 1

[Kevin Blighe]

If you need 'raw' data FASTQ files and do not have access to such data at the TCGA or ICGC, then it would be easier to search for samples via:

• EGA (however, typically, EGA-deposited data is controlled in some way)
• SRA
• ENA

Typically, searching at SRA first can be useful, but then downloading the data for these from ENA (by searching for the SRA BioProject ID at ENA). I say this because ENA makes the data available as FASTQ, whereas, with SRA, the data is encoded in a very annoying way. In relation to these, please see this tutorial: Fast download of FASTQ files from the European Nucleotide Archive (ENA)

Please also see these other answers:

• A: Where Can I Find Data Sets Of Cancer Publicly Available?

Kevin