Hi,
I was wondering what people is using to download huge amounts of experiments in SRA format. I'm currently using a home made script that downloads everything and classifies it using the runinfo table that can be downloaded from the sra selector (http://www.ncbi.nlm.nih.gov/Traces/study/?go=home)
I find this extremely cumbersome but is the best option I got. Is there any download manager I'm missing? What do you people use to download a (big) set of experiments.
Well I start with something like this
esearch \
-db sra \
-query PRJNA40075 | \
efetch \
--format runinfo | \
cut -d ',' -f 1 | \
grep SRR | \
head -5 | \
xargs fastq-dump -X 10 --split-files
Also seen here: How to download raw sequence data from GEO/SRA
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written
by
Istvan Albert
If you plan to use BWA mem make sure to set the --origfmt flag for the fasts-dump Aligning paired end fastq files dumped from SRA
•
written
by
Zev.Kronenberg
never ran into this myself - though I do download/process paired end reads - there is probably more to it, perhaps the way the sra file was built.
•
written
by
Istvan Albert
Maybe the SRAdb package from R/Bioconductor can help? As mentioned in, e.g. this A: SRX from SRR IDs . It will help deciding what needs to be downloaded.
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