I need cancer databases suggestion
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UGUR • 0
@d4ce494d
Last seen 7 days 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 ? Thanksenter image description here

#ccle #tcga #cancer • 89 views
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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 ]
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