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nsheff / LOLA

Locus Overlap Analysis: Enrichment of Genomic Ranges
http://code.databio.org/LOLA
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cistrome_mm10 #29

Open byerscan opened 5 years ago

byerscan commented 5 years ago

Database downloads include cistrome files for hg19 and hg38 but not for mm10. The database downloads page on databio site describes a LOLACore for mm10 including Cistrome, but when I downloaded the region core database, cistrome is missing from mm10. Is this a future endeavor? Do you plan on including cistrome as part of LOLAcore for mm10 soon?

In the meantime I have contacted Cistrome directly to get access to the files for mm10 and plan to create a custom database to run with LOLA. Hope to hear about future plans with LOLACore for mm10!

nsheff commented 5 years ago

Thanks for pointing this out -- you are right. I think they were in there at one point, but they somehow are not anymore... I guess I didn't notice because I haven't used LOLA much for mouse!

I could construct this mm10 database, as I do still have the original files I downloaded, but if you can get the files from cistrome directly for mm10 it would probably be much more up-to-date, as my download was from 4 years ago... so it's probably best to go that route. If you do create a custom database, if you can pass that on to me I'd be happy to update the primary database (then you could use lolaweb, for example).

byerscan commented 5 years ago

I would be happy to share the Cistrome files, but they came with a contingency of not sharing. I will contact them again and ask if it would be OK for LOLA to use; see terms of usage below:

Term of usage:

CistromeDB, also known as Cistrome Datasets Browser, is a Database of ChIP-seq, Chromatin Accessibility data. You may download the content of the Database free of charge under the following conditions:

  1. You agree NOT to make the CistromeDB (or any part thereof, modified or not) available to anyone outside your research group. "Make available" includes leaving the data where it may be accessible to outside individuals without your direct knowledge (e.g. on a computer to which people outside your group have login privileges), as well as directly providing it to someone.
  2. You agree NOT to build another website using the download data. Please contact us if you are going to.
  3. You agree NOT to use the download data for proprietary analysis.
  4. You agree to properly cite the Database and its specific, original contributions if directly related to your work.

Zheng R, Wan C, Mei S, Qin Q, Wu Q, Sun H, Chen CH, Brown M, Zhang X, Meyer CA, Liu XS. Cistrome Data Browser: expanded datasets and new tools for gene regulatory analysis. Nucleic Acids Res, 2018 Nov 20. Doi: 10.1093/nar/gky1094

Mei S, Qin Q, Wu Q, Sun H, Zheng R, Zang C, Zhu M, Wu J, Shi X, Taing L, Liu T, Brown M, Meyer CA, Liu XS. Cistrome data browser: a data portal for ChIP-Seq and chromatin accessibility data in human and mouse. Nucleic Acids Res, 2017 Jan 4;45(D1):D658-D662. Doi: 10.1093/nar/gkw983).

  1. You certify that you are authorized to accept this agreement on behalf of your institution.
  2. All members of your group with access to the Database agree to the same conditions

Maybe a simple request will let me go around these restrictions.