where to find cancer data

Question

[shubhamkumbhar420]

I am looking for cancer data(especially for lung cancer) for my project. where can I get fastq files for that?
Thanks in advance.

Answer 1

[ATpoint]

This has been asked many times before, please use the search function.

E.g. Where to Download Cancer Raw Reads (fastq)?

Cancer sequencing data as fastq are hosted e.g. at TCGA/ICGC and dbGaP. databases. You need to read papers that created them and find the respective accessions. Be aware though that these are always access-restricted so your PI must apply for access via your institution, then access might be granted upon reasonable request. This is not optional and there is most likely no way around this. This is going to take weeks though as the application gets formally reviewed, maybe rejected first asking for edits etc, which is why you should always work with an experienced supervisor who has knows how things are going in the field. From your previous question I take that you are doing an undergraduate project. If you have no background so far, and no data at hand so far, this is likely to be an extremely cumbersome process. Get a supervisor!

[shubhamkumbhar420]

Thank you for your suggestion! I will get a supervisor.

[shubhamkumbhar420]

Can I use the SRA database?

[ATpoint]

You can try but most likely are not going to find much because, as said, most are in access-restricted databases such as dbGaP.