Question: Download SRA files for a specific Transcription factor (e.g GATA3) from GEO
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gravatar for elpavloss2
23 months ago by
elpavloss20
elpavloss20 wrote:

Hi!,

I want to download several SRA files from different GEO studies, both the input and the replicates data. The last month I spent a lot of hours doing that manually. I decided to find how I could do it automatically. I read this manual from NCBI https://www.ncbi.nlm.nih.gov/books/NBK179288 and understand now how I can use esearch, efetch in general.

  1. Is it possible to get all the IDs relative with a TF and then download the SRAs?
  2. If the 1st question will be solved, how I can distinguish the control/input files from the replicates?

My background is mathematics but lately involved in TFBS analysis, so my knowledge in this domain is probably not enough to get an answer all alone.

Thank you for your time!

chip-seq sequence • 592 views
ADD COMMENTlink written 23 months ago by elpavloss20

Are you looking for all experiments that have done differentiation expression with GATA3? The SRA samples do not have specific tags for transcription factors but you could search for "GATA3" in the study name for example, and use search to download those studies.

ADD REPLYlink written 23 months ago by Joseph Hughes2.6k
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