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.
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 SRAnever 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.