Could I find any tutorial of CERaTor?

[wangxuann1995]

Hi Zhiyuan,

Many thanks for bringing CREaTor to us! I believe it could promote our understanding and build the connection between CRE and target genes.

However, could you help to give some tutorials to run CREaTor? I followed the README and I could only find one pkl file in the examples dir. After I run the ./run_example.sh, it only returns result like this:

@ZhiyuanChen

Sincerely,
Xuan

[ZhiyuanChen]

Hi Xuan,

Thank you for your interests in our work!

Could you please be more specific with your question?

The run_example.sh just pass the example.pkl to https://github.com/DLS5-Omics/CREaTor/blob/main/CREaTor.py.

[wangxuann1995]

Hi Zhiyuan,

Thanks for your reply.

I hope to understand the CRE's target genes, so from my understanding I think CRETor could interpret the cCRE-gene and cCRE-cCRE interactions.

I wonder what I should do if I begin with RNA-Seq and ChIP-Seq (H3K27ac)? For example, I check the example.pkl you mentioned in tutorial, which contains E_ge, E_chp, E_pos, G_pos, G_gpos. Could you help to explain how could I convert RNA-Seq and ChIP-Seq to pkl file which I could pass to CREaTor.py?

Sincerely,
Xuan

[wanghan4034]

+1, it will be great if providing the raw data processing file

[Teddiess0217]

I wonder what G_pos, G_gpos represent?

[yang-dongxu]

+1, it will be great if providing the raw data processing file.

[aaachina]

i suppose that the run/example.sh is not the real raw data,and the DNA sequences are not like the one-hot code?Also i could not find the pre-processing of the raw data?