Lee Katz

I am the senior bioinformatician in the Enteric Diseases Laboratory Branch at CDC. In my free time, I try to be a good husband and parent, and in my imaginary free time, I podcast with my co-hosts on the Micro Binfie podcast.

less than 1 minute read

I have been really excited by the new-ish edirect utilities.  I thought I’d put out my snippets and encourage anyone to show theirs too.  I haven’t found a lot of great snippets for what I exactly need (although it makes sense because there are so many uses for it). 

Given a biosample access, find the SRR number

esearch -db sra -query $SAMN | efetch | xtract -pattern IDENTIFIERS -element PRIMARY\_ID  | grep SRR

Using sratools to get an SRR.  This one doesn’t really belong since it’s not edirect, but it’s important to note that this is the correct way to deal with SRA, once you know the identifier that you want to download.

fastq-dump --split-files -O $NAME $SRR

Updated:

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