cistrome_mm10 about lola HOT 2 OPEN

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).

from lola.

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).

5. You certify that you are authorized to accept this agreement on behalf of your institution.
6. 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.

from lola.