database - selection of library preparation

Question

[dentepre]

Hi,

I'm trying to find sequencing raw data in SRA database, but obtained only from rRNA depletion libraries (and only from humans). How should I set the parametes of serch to obtain only this type of data? In "advance search" bookmark there are filter like organism, platform etc but there is no option fo library preparation...

Thanks, dentepre

[GenoMax]

Many of the datasets should be rRNA depleted. How many do you need? You could look some publications up and then get those datasets if the rRNA depletion has been done.

[dentepre]

I would prefer to choose datasets directly from the database, not from publications etc. Type of library preparation is ofc not the only criterium of searching, but I need something more "automatic" than just looking for the keywords for example in PubMed.

[GenoMax]

You are limited by what is provided in the metadata by SRA (ultimately the submitters). So consider that as you devise a search strategy. You can use the NCBI eutils, grab a set of SRA records and see what you could use for your search.