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splicing and feature maps for RBPs
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Final set of reproducible significant peaks - encode 3 #8

Closed gouthamatla closed 3 years ago

gouthamatla commented 3 years ago

Hi All,

May I know where can I find the final set of peak calls from ENCODE 3 RBP data ? I could find individual replicates but I did not find replicate-merged IDR peaks.

https://www.nature.com/articles/s41586-020-2077-3

Thanks, Goutham A

byee4 commented 3 years ago

You can find all reproducible peaks from ENCODE3 on the encodeproject.org site. You may need to convert these to bigBed format to use rbp-maps, but it should be a simple bed -> bigBed conversion.

Here is an example link from the site. If you have any experience parsing out JSON files, I would suggest using their API, otherwise you can use the experiment matrix (ie. https://www.encodeproject.org/report/?type=Experiment&control_type!=*&status=released&perturbed=false&assay_title=eCLIP&biosample_ontology.term_name=HepG2&files.file_type=bed+narrowPeak&assembly=hg19 )

example reproducible peaks for RBFOX2 (HepG2):

https://www.encodeproject.org/files/ENCFF871NYM/@@download/ENCFF871NYM.bed.gz