add mm39 genome

[fabio-t]

No description provided.

[fabio-t]

should be fine, merged to developed but I haven't tried running something on it.

@lzj1769 This was requested for HINT-ATAC, so maybe you could try running the program on mm39 to see it produces similar results to mm10? It's pushed to develop now.

Here's the changeset if you want to have a look: e9d7ca9

[lzj1769]

@lzj1769 This was requested for HINT-ATAC, so maybe you could try running the program on mm39 to see it produces similar results to mm10? It's pushed to develop now.

Thanks @fabio-t, I will check it out.

[lzj1769]

mm39 is added to the latest version and this issue is closed now.

[palmiralg]

Hello. I've just installed RGT to perform HINT-ATAC on mouse ATAC-seq data that has been aligned to mm39. @lzj1769 said

"mm39 is added to the latest version and this issue is closed now."

but when I look at the rgtdata folder, the mm39 assembly isn't there.

python setupGenomicData.py --mm39
usage: setupGenomicData.py [-h] [--all] [--hg19] [--hg38] [--mm9] [--mm10] [--zv9] [--zv10] [--hg19-genome-path STRING] [--hg38-genome-path STRING]
                           [--mm9-genome-path STRING] [--mm10-genome-path STRING] [--zv9-genome-path STRING] [--zv10-genome-path STRING] [--hg19-gtf-path STRING]
                           [--hg38-gtf-path STRING] [--mm9-gtf-path STRING] [--mm10-gtf-path STRING] [--zv9-gtf-path STRING] [--zv10-gtf-path STRING] [--hg38-rm]
                           [--hg19-rm] [--mm9-rm]
setupGenomicData.py: error: unrecognized arguments: --mm39

Could you please help me? Thank you

[lzj1769]

Hi @palmiralg

We added this feature to our develop branch, and have not released it officially.

To use it, please install rgt from the source code as follows:

git clone [email protected]:CostaLab/reg-gen.git
cd reg-gen
git branch checkout develop
pip install ./

We will do the release soon.

Best,
Zhijian

[palmiralg]

I see, thank you for your quick answer!