GRCh38 / hg38 stratification BED files

[blmoore]

Do the BED files under resources/stratification-bed-files exist for GRCh38? If so it would be great if they could be added to the repo

[jzook]

Not yet - I've created some of these, so I'll work on creating the rest of them and add them to the resources.

[isthisthat]

Any timelines on this? Would you accept a PR e.g. for the GCcontent, LowComplexity and mappability tracks (which look straightforward) on this version of the genome for instance: ftp://ftp.ensembl.org/pub/release-90/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa.gz

What's the preferred naming convention / folder structure?
Thanks a lot!

[EvanTheB]

Hello, any update on this? Is it possible to translate the beds? or do the resources that created them in the first place exist?
Thanks

[jasper1918]

Curious if anyone else has compiled an hg38 resource similar to those found here? Thought I would ask before I jump in to start creating my own and would prefer these be standardized for all to use.

[jzook]

Sorry for the delays in developing this and for missing this discussion. We plan to start working toward making a standard set for GRCh38 available by the end of 2018. If you're interested in helping with this or have already done this, we'd definitely be happy to hear what you've done.

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On Wed, Sep 12, 2018 at 4:26 PM Jeff S Jasper ***@***.***> wrote: Curious if anyone else has compiled an hg38 resource similar to those found here? Thought I would ask before I jump in to start creating my own and would prefer these be standardized for all to use. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#27 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ACU6dkJ3ozmAZgbVlFVujfhg3_Z4LfcIks5uaW3jgaJpZM4MP5LD> .

[kwdunaway]

Hi, I'm also interested in getting this data in hg38. What files have you created so far? Even a partially completed list is better than nothing.

[jzook]

I apologize for the delays in completing this due to the federal government shutdown. We do have a small subset of some of the most important large subsets, which we used in our recent manuscript ( https://doi.org/10.1101/281006, in press in Nature Biotechnology), on github here: https://github.com/jzook/genome-data-integration/tree/master/NISTv3.3.2/filtbeds/GRCh38 We hope to make additional files available in the near future. We have also found the various UCSC RepeatMasker files to be useful.

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On Fri, Jan 25, 2019 at 1:38 PM Keith Dunaway ***@***.***> wrote: Hi, I'm also interested in getting this data in hg38. What files have you created so far? Even a partially completed list is better than nothing. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#27 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ACU6doXiDb02DCy6ZQRB4IJydq4g89kiks5vG08MgaJpZM4MP5LD> .