"DNase Hi-C on tissues" (from mm10 mouse brain) available for mm39?

[Rebekah Rashford]

Hello! I hope you are well. I'm wondering if the publicly available track "DNase Hi-C on tissues" from mm10 (from brain tissue as it comes up when "brain" is searched) could be available / lifted over from mm10 to mm39, please? Is this possible?

Best,

rr

[lid...@gmail.com]

Hi Rebekah,

Yes, sorry for that!

We have 2 servers have disk failure, one is fixed, another one is still not online yet. I will reply you here once it's back online.

[Rebekah Rashford]

Thank you! I will look out for your update.

------------------------------------------------

Rebekah Rashford, PhD | Peña Lab

Princeton Neuroscience Institute | Office: 176G

Princeton University

rash...@princeton.edu

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[Rebekah Rashford]

Hello! I'm wondering if those servers have come back online, yet? 

All best,

Rebekah

------------------------------------------------

Rebekah Rashford, PhD | Peña Lab

Princeton Neuroscience Institute | Office: 176G

Princeton University

rash...@princeton.edu

[lid...@gmail.com]

Hi Rebekah,

Sorry I forgot to reply here. Those tracks should be back, the server is still broken, but we managed to move the files to a different server.

Let me know if you cannot load the tracks you wanted.

Thanks!

[Rebekah Rashford]

Thank you for the quick reply! 

I see the "(2025) 4DN datasets (1348 tracks)" in the Public Data Hub in the mm10 genome browser, but I don't see it in the mm39 browser. Is it possible to load or liftover the data to be used in the mm39 browser? (Or, if not all the tracks, just the "DNase Hi-C on tissues" track to mm39? [Data Hub: 4DN datasets, Sample: brain, Assay: DNase Hi-C, Format: hic])

Thanks again for all your help!

rr

------------------------------------------------

Rebekah Rashford, PhD | Peña Lab

Princeton Neuroscience Institute | Office: 176G

Princeton University

rash...@princeton.edu

To view this discussion visit https://groups.google.com/d/msgid/epgg/59ebdb92-c052-443e-bcf9-f9c0c4232a6cn%40googlegroups.com.

[lid...@gmail.com]

Hi Rebekah,

I don't think liftOver-ing hic files is reasonable...It might be ok to start from contact matrix, lifting and then convert to hic files.

The data are hosted at 4dn data portal, https://data.4dnucleome.org/, if you don't have the storage, we are happy to host for you.

You might need to process the files yourself, we are happy to help with the storage, hosting and building the datahub json file.

Hope this helps.

[Rebekah Rashford]

Yes, this is so helpful! Thank you so much. Apologies for the suggestion of lifting over the hic file -- I'm not well-versed in this area of analysis! 

I think lifting and then converting the contact matrix is a perfect idea. I do anticipate I'll need some help with the storage, hosting, and building the datahub json file! The file contact matrix file I'm hoping to lift + convert is "4DNFIQ48NYOW" from this experiment: https://data.4dnucleome.org/experiment-set-replicates/4DNESRWDFFF8/#details  . What should be my first step?

All best,

Rebekah

------------------------------------------------

Rebekah Rashford, PhD | Peña Lab

Princeton Neuroscience Institute | Office: 176G

Princeton University

rash...@princeton.edu

To view this discussion visit https://groups.google.com/d/msgid/epgg/c9f4deca-306b-47bb-986d-8d2a4f91c741n%40googlegroups.com.