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sldrcyang / nMAGMA

Codes and data used in nMAGMA, an approach to intergrate Hi-C, eQTL and gene networks inferred from WGCNA into original MAGMA annotation.
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Annotate file from Hi-C file #1

Open kvshams opened 4 years ago

kvshams commented 4 years ago

Hi authors, Congratulations for the article and nice work. How did you create/process the raw Hi-C files to create annotate files. It would be really helpful to include the data pre/post process scripts also in the repo. Thanks, Shams

sldrcyang commented 4 years ago

Dear Kvshams,

Thanks for your advice, we will consider to provide a more detailed script about the process. For creating Hi-C annotate files, we first annotated SNPs to REs based on their physical location using MAGMA directly, then assigned the SNPs to genes via SNP-to-RE annotations and RE-gene regulatory pairs (more details can be seen in Methods and Materials of nMAGMA paper).

Yang

jamesdalg commented 3 years ago

Yes. If you were able to, that would be wonderful. H-MAGMA doesn't provide scripts on how to process the data and doesn't really describe concretely how they processed their data. It's just frustrating because, even though it's a nature neuroscience paper, it's not reproducible and is largely useless except for the small amount of tissues they provide. If nMAGMA were to do this, it could increase your citations and h-index from users who can then use your work.

sldrcyang commented 3 years ago

Thanks for your advise. We have already provided a script named as Main_script.txt on how to conduct nMAGMA step by step. I hope that will be useful for you. If you have any question or suggestion, please do not hesitate to contact me.