How to download a large amount of NGS metadata for studies?

Question

[RafaelMP]

Hi All,

I am starting my project with RNA-Seq in human. I've worked with SRA data for other species, but the present work is much bigger.

I do not know if there is a site that provides the information I want. I want to get two tables (txt or CSV) of experiments (with information to download the files later):

1- paired-end reads, > 75 BP and a specific cellular tissue;

2- paired-end reads, > 75 BP, a specific cellular tissue and only data from normal condition;

Thanks!

Answer 1

[Istvan Albert]

This is really an issue of whether the data is annotated properly, if it is you can do a:

esearch -db sra -query "your query goes here" | efetch -format runinfo

[Ying W]

More info about esearch here.