Question

I need cancer databases suggestion

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UGUR • 0

@d4ce494d

Last seen 22 months ago

Turkey

Hello Guys,

I need a metastatic cancer line data (if it is possible WGS) that is obtained from the one-patient's purified biopsy results derived from different regions (like lung, bladder). I need this data to investigate cancer evolution to apply some popgenome analyses. I guess I've found the samples of Cancer Cell Line Encyclopedia (CCLE) on the SRA however I cannot download them through prefetch command on bash terminal I'm getting an error on attached file, I guess it stems from my access permission.

Any guys can help me to suggest me any database I need or say any alternative way to download of CCLE data from SRA ? Thanks enter image description here

#ccle #tcga #cancer • 1.3k views

ADD COMMENT • link updated 22 months ago by Marcel Ramos 690 • written 22 months ago by UGUR • 0

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Cross-posted: https://www.biostars.org/p/9527735/

ADD REPLY • link 22 months ago Kevin Blighe ★ 3.9k

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It looks like it is a certificate issue. I was able to download the resource using prefetch 3.0. Make sure to update your SRAtoolkit.

./prefetch SRR8657722

2022-06-21T13:42:27 prefetch.3.0.0: Current preference is set to retrieve SRA Normalized Format files with full base quality scores.
2022-06-21T13:42:27 prefetch.3.0.0: 1) Downloading 'SRR8657722'...
2022-06-21T13:42:27 prefetch.3.0.0: SRA Normalized Format file is being retrieved, if this is different from your preference, it may be due to current file availability.
2022-06-21T13:42:27 prefetch.3.0.0:  Downloading via HTTPS...
2022-06-21T13:42:52 prefetch.3.0.0:  HTTPS download succeed
2022-06-21T13:42:52 prefetch.3.0.0:  'SRR8657722' is valid
[ truncated ]

ADD REPLY • link 22 months ago Marcel Ramos 690