I am intending to work with some public transcriptome data from a study GSE61476. I actually do not want to download the data in our HPC or even on my local computer. I have a script that usually pings the FTP server of the EBI FTP archive and pulls the fastq for the SRA data. However am unable to understand if this data is there in the EBI FTP archive or not. Is there a portal in EBI where I can search for the SRR/ERR/DRR ids that lead me to the proper FTP locations for this data? I have a feeling that I am missing something since I see in this link that the fastq files are there but the column for the FTP submitted is blank. Does that mean that EBI has not put it in their public FTP server the fastq for this study? Is there a way to have this data somewhere in EBI ftp link which I am missing so that I can download them on the fly and perform quantification?
I was expecting to have for this particular study something from here
Am I missing something or this data is not yet in the public FTP of EBI archive? Also if it's there then how do find the corresponding SRR/ERR/DRR id that leads me to that FTP folder? If anyone has some suggestions it would be great.
thank you very much so probably I have to use the XML accession code and these data is not yet deposited in the EBI FTP archive which I am interested in. This is what I understand then.
Hi, Not a direct answer but may be of help. I like SRA run selector very much, It gives all information about the study in one place (cases,control, insertsizes.... ). For example (https://www.ncbi.nlm.nih.gov/Traces/study/?acc=GSE61476&go=go) . For download all is needed is the column RUN of the exported file (SRR ids). The URLs for downloaded can be constructed by a script using the SRR ids has explained here from ENA database.