Hi there folks, I am trying to download SRA files from a dataset I compiled from the NIH Roadmap Data Matrix. The problem is that the dataset spans about 50-60 files. I have little intend of downloading them by hand and I thought a quick wget would help but for some reason each link provided just holds another subdirectory and does not point to the locations of the actual *.sra files which makes it a lot harder to download them:
Sample1 ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX099/SRX099571 Sample2 ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX040/SRX040594
My script so far does this:
while read name files; do mkdir $name wget $files -P /$name/ done < List
I tried some different approaches like (and many others):
wget --no-parent -r -l1 ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX099/SRX099571/
My list just contains my sample names and the links which were provided by the data matrix. But wget seem to have problems accessing the subdirectory with the *.sra file without specifying the path explicitly.
If anybody has an idea on how to solve this I would be eternally grateful. Since at this time I probably would have been done downloading them by hand.