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.
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 likersync://ftp.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX212/SRX212665
.Alternative way is:
Runinfo
we can mapGSMnnn
to list ofSRRnnn
SRRnnn
usingfastq-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.