Is there a file information dictionary for files downloaded from ENCODE through batch download?
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2.1 years ago
burcakotlu ▴ 40

e.g:

I have downloaded ENCFF212JTP.bigwig and many others using batch download.

Can we learn that ENCFF212JTP.bigwig comes from H3K27ac histone marks from MCF-7 cell line using a dictionary in code?

Instead of visiting web page for each file https://www.encodeproject.org/files/ENCFF212JTP/ manually and learning one by one?

Thanks

ENCODE batch downoad • 427 views
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2.1 years ago

If you have followed the proper protocol for batch download then there must be a file name Metadata.tsv in each batch. This metadata file contains following information: File accession File format Output type Experiment accession Assay Biosample term id Biosample term name Biosample type Biosample organism Biosample treatments Biosample treatments amount Biosample treatments duration Biosample genetic modifications methods Biosample genetic modifications categories Biosample genetic modifications targets Biosample genetic modifications gene targets Biosample genetic modifications site coordinates Biosample genetic modifications zygosity Experiment target Library made from Library depleted in Library extraction method Library lysis method Library crosslinking method Library strand specific Experiment date released Project RBNS protein concentration Library fragmentation method Library size range Biological replicate(s) Technical replicate Read length Mapped read length Run type Paired end Paired with Derived from Size Lab md5sum dbxrefs File download URL Assembly Genome annotation Platform Controlled by File Status s3_uri Audit WARNING Audit INTERNAL_ACTION Audit NOT_COMPLIANT Audit ERROR

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Thanks. That metadata.csv is also downloaded. But I was not aware of. Thanks, again.

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