How to get public cancer RNA-seq data?

Question

[kenneth8903]

Hi

I am master degree student of Bioinformatics. My term project is analysis of lung adenocarcinoma variant calling and structural variation analysis. So I need the fastq files of that cases. I have https://commons.era.nih.gov/ PI accounts of my professor that allow it and I search dbGaP and SRA. How to get Fastq file of that cases?

Answer 1

[craig]

Using Repositive will (currently) give you 3,112 datasets using the term "cancer RNA-seq"

You can view the results here (you don't even need an account): https://discover.repositive.io/datasets/search?query=cancer%20RNA-Seq

Having a quick look, these 3,112 datasets come from 10 different databses, including SRA and dgGaP but also Array Express, InsilicoDB, Methycancer, Xpressomics, Gene Expression Atlas, GEO, GigaDB and Horizon Discovery.

Answer 2

[alolex]

Your advisor will need to request access to the TCGA protected data via dbGaP, and list you as a collaborator. Once approved you will need to download the key file through dbGaP Authorized Access Login. Then go to CGHub and follow the instructions to download their GeneTorrent software (https://cghub.ucsc.edu). This is the ONLY way to access raw sequencing data, including FASTQ files. Once all this is done you can use the CGHub Browser to identify the cases you want and create a manifest XML file. This file can be passed to the GeneTorrent download program (gtdownload) and it will download the files you need. Hope this helps if you haven't already figured it out.

Answer 3

[Michael]

https://tcga-data.nci.nih.gov/tcga/tcgaAccessTiers.jsp

Does this help?

[kenneth8903]

Thanks your reply.

But I know that information and I wanna more detailed practical issue.

Maybe this problem needs to study manual and tutorial.

Answer 4

[Antonio R. Franco]

Look into the NCBI GEO database. It is full of cancer data

Answer 5

[matt.newman]

You may want to check out OncoLand: http://www.omicsoft.com/oncoland-service. This won't get you access to the FASTQ files, but it's a great tool for accessing Oncology data.

Answer 6

[j.salys]

To get GEO data using python you can use GEOparse package. For more details. Check out this blog post: http://friendlypython.herokuapp.com/2018/6/analysis-geogene-expression-omnibus-data/