Tweet
Hi, the SRA naming conventions are a bit frustrating. I have two SRA submission accession numbers, from a publication (SRAnnnn). I want to obtain a list of SRR numbers (or SRX and similar) associated with these submissions.
I have tried the SRAdb R package from Bioconductor, but the database (SRAmetadb.sqlite.gz) that is downloaded appears to contain no tables so the other scripts in the package just fail. Is there an online database that I can query?
Also what is the best way (command-line wise) to download a set of files given their SRR number? I have limited internet access, so I plan to use bash scripting with wget, using:
wget -O SRRnnnn.fastq.gz "http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=dload&run_list=SRRnnnn&format=fastq"
as suggested on the biostar forum. Combining the above with the unix 'at' command.
I have tried the SRAdb R package from Bioconductor, but the database (SRAmetadb.sqlite.gz) that is downloaded appears to contain no tables so the other scripts in the package just fail. Is there an online database that I can query?
Also what is the best way (command-line wise) to download a set of files given their SRR number? I have limited internet access, so I plan to use bash scripting with wget, using:
wget -O SRRnnnn.fastq.gz "http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=dload&run_list=SRRnnnn&format=fastq"
as suggested on the biostar forum. Combining the above with the unix 'at' command.
