Re: [encode-help] Help Understanding Encode Terms

[Meenakshi Kagda]

Hello Anthony, 

Thank you for your interest in the ENCODE data.

The dataset you are referring to is here: https://www.encodeproject.org/experiments/ENCSR000EIK/ and the prefix "ENCSR" refers to a dataset/experiment.

The other id that you have provided ENCFF110QCM with the prefix "ENCFF" is a file identifier. However there seems to be a typo in the id you have provided. I think you are referring to ENCFF110QGM and the exact file details can be found here: https://www.encodeproject.org/files/ENCFF110QGM/ (bigwig file).

Just FYI: the file is not equivalent to a sample in terms of ENCODE. Below is a screenshot that exemplifies the same:

In this case, the sample is  (ENCBS155AAA)- Homo sapiens male adult (35 years) frontal cortex tissue. And the file ENCFF110QGM is derived from the fastqs that were created after analyzing this sample.

I am not exactly sure about how the UCSC plug-in works. I think someone from UCSC will be better able to assist you with your specific question (cc'd here and also can find more information here: https://genome.ucsc.edu/contacts.html)

Let me know if you have any further questions from the ENCODE side.

Thanks,

Meenakshi

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From: encode-help <encode-he...@lists.stanford.edu> on behalf of Anthony Mendoza via encode-help <encod...@lists.stanford.edu>
Sent: Tuesday, October 15, 2024 1:44 PM
To: encod...@lists.stanford.edu <encod...@lists.stanford.edu>
Subject: [encode-help] Help Understanding Encode Terms

 

Hi Encode Team,

I wanted some help understanding the difference between an identifier and a specific experiment in ENCODE. I have an identifier ENCFF110QCM and an Encode experiment ENCSR000EIK. From my understanding, the encode identifier corresponds to a specific sample within the encode experiment whereas the encode experiment encompasses all sample info associated with the specific sample identifiers? If this is the case, would you happen to know if there's a specific way I can search the UCSC genome browser based off of the Encode identifier alone without the Encode experiment so that I can verify that it has a UCSC plug-in available for that identifier? Is it the case that if an Encode experiment has a UCSC plug-in that all identifiers within it will be available through the UCSC plug-in?

Sincerely,

Anthony Mendoza