multiple SRR in a particular FTP conflict

Question

[firatuyulur]

Hi all, It might be a silly question but I need to understand this. I am working on some ChIP-Seq data and while I was downloading the SRA from geo, when I clicked on ftp at very bottom there are multiple SRR coded folders, each holding an SRA file inside. The question is, there is only one SRR folder, and one SRA file inside of it, in the other samples' ftp's generally with size ~1gb. However, now I am facing 3 sra files with ~170mb size. Can someone explain whats what? Cheers

[GenoMax]

Your experiment has three runs/samples in it.

[firatuyulur]

yes, thats helpful but the thing is 8million spots for a chipseq data is kind of a low. Should I process them separately and then merge them? or merge the fastqs? I agree that there are 3 runs but not sure whether they are replicates, the three seem to be complementary ?

[EagleEye]

This is the maximum information I could see for this dataset. Atleast from the methods part, they did not explain anything about analyzing replicates (Chip-seq).

http://www.nature.com/nature/journal/v503/n7475/extref/nature12644-s1.pdf

SOURCE: http://www.nature.com/nature/journal/v503/n7475/full/nature12644.html

Answer 1

[EagleEye]

It looks like you got three runs for same Chip-seq sample,

http://sra.dnanexus.com/?result_type=Experiment&show=25&q=SRX212186

http://sra.dnanexus.com/experiments/SRX212186/runs