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CostaLab / reg-gen

Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.
https://reg-gen.readthedocs.io/
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rgt shifting #233

Closed Andi964 closed 1 year ago

Andi964 commented 1 year ago

Hello, i have two questions regarding the rgt-hint footprinting function:

A) Does this command using the --atac-seq argument include proper Tn5-shifting, or do we have to shift the data before? B) Can/should the --bias-correction argument be applied for atac-seq data?

Best, Andreas

lzj1769 commented 1 year ago

Hi,

Yes, the —atac-seq argument will automatically enable Tn5 shifting, so you don’t need to do it before.

By default, —atac-seq will also include the bias correction.

Best, Li

Zhijian Li Institute for Computational Genomics RWTH Aachen University Pauwelsstrasse 19 Aachen, Germany On Nov 17, 2022 at 21:06 +0800, Andi964 @.***>, wrote:

Hello, i have two questions regarding the rgt-hint footprinting function: A) Does this command using the --atac-seq argument include proper Tn5-shifting, or do we have to shift the data before? B) Can/should the --bias-correction argument be applied for atac-seq data? Best, Andreas — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you are subscribed to this thread.Message ID: @.***>