using SQLlite3
https://edwards.sdsu.edu/research/getting-data-from-the-sra/
using linux wget
details in http://seqanswers.com/forums/archive/index.php/t-30625.html
wget -r -nd -nH ftp://file_address
for example,
wget -r -nd -nH ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByStudy/sra/SRP/SRP103/SRP103124
Address is changed : edit 20210720
https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11780909/SRR11780909
To download specific SRA files in the list
Store the SRR096001-SRR096999 #s that would want to download in a file:
for example:
cat > SRR_2_download
SRR096023
SRR096072
SRR096074
for i in $(cat SRR_2_download);do wget -r -nd -nH ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/litesra/SRR/SRR096/$i/*; done
for i in $(cat SRR_2_download);do wget https://sra-pub-run-odp.s3.amazonaws.com/sra/$i/$i; done
This will download the specific SRA files that are listed in the file SRR_2_download
using R
details in www.biostars.org/p/93494/
Run R source('http://bioconductor.org/biocLite.R') biocLite('SRAdb') library(SRAdb) biocLite('DBI') library(DBI) srafile = getSRAdbFile() # Download & Unzip Last Version Of SRAmetadb.Sqlite.Gz From Server to working directory # Once you download SRAmetadb.Sqlite.Gz, set SRAmetadb.sqlite file to variable srafile # SRAmetadb.Sqlite.Gz is big. Re-download if you need updated version srafile <- 'SRAmetadb.sqlite'con = dbConnect(RSQLite::SQLite(), srafile) listSRAfile('SRP026197',con) getSRAfile('SRP026197',con,fileType='sra') ## dump SRA file to fastq.gz (required SRAtoolkit) Run in linux fastq-dump -O /output/dir --gzip ./SRR2047462.sra #sra file dump to SRR2047462.fastq.gz
library(GEOquery)
gse <- getGEO('GSE48138') # retrieves a GEO list set for your SRA id.
## see what is in there:
show(gse)
# There are 2 sets of samples for that ID
## what you want is table a with SRR to download and some sample information:
## lets see what the first set contains:
df <- as.data.frame(gse[[1]])
head(df)
