Cancer exome sequences
1
0
Entering edit mode
21 months ago

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??

sra cancer sequence • 329 views
ADD COMMENT
1
Entering edit mode
21 months ago

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:

Kevin

ADD COMMENT

Login before adding your answer.

Traffic: 1988 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6