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lingxusb / Riboformer

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Question about creating wig files for data_processing.py #2

Closed DaehwaYoun closed 6 months ago

DaehwaYoun commented 7 months ago

I am trying to run Riboformer, but I am having trouble creating required wig files. So, I want to ask whether there is any recommended tool for creating fixed step wig files for data_processing.py from BAM files.

lingxusb commented 7 months ago

I am trying to run Riboformer, but I am having trouble creating required wig files. So, I want to ask whether there is any recommended tool for creating fixed step wig files for data_processing.py from BAM files.

Thank you for your question. I think you can go with any published tool that you are comfortable with. For bacteria, I would recommend the Buskirk Group's codes: github, original publication is here

I heard other people has used DeepTools. The Lareau lab and the Wallace lab have developed riboviz and the publication is here

I hope these information helps. Please let me know if there is any further question.