GEO downloader doesn't work due to NCBI API changes - Githubissues

JetBrains-Research / washu

Reproducible and scalable technical pipelines for ChIP-Seq and RNA-Seq processing

https://artyomovlab.wustl.edu/aging

MIT License

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GEO downloader doesn't work due to NCBI API changes #54

Open iromeo opened 6 years ago

iromeo commented 6 years ago

E.g. we cannot batch download files by GSMxxx id using GSMnnn to SRXnnn mapping and NCBI FTP /ftp.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX . So we cannot use aspera or rsync with urls like rsync://ftp.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX212/SRX212665.

Alternative way is:

Using Runinfo we can map GSMnnn to list of SRRnnn
Download SRRnnn using fastq-dump (https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=toolkit_doc&f=fastq-dump) as GEO SRA team suggests or using SRR related roots at GEO ftp.

We need to change scripts/geo_rsync.sh to support that.