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Hello,
First of all, thank you for developing chromap. It saves me tons of mapping time :) For a feature request, I am wondering if the chromap could generate sth like a summary report (at the cel…
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Hi Felix,
Have you ever seen methylation bias due to tagmentation based WGBS libraries?
We performed some WGBS using the EZ DNA Methylation Kit which used Tn5 and observed a strange M-bias profile o…
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Hi team,
Thanks for the amazing tool!
I am currently working on a modified protocol of ATAC and would like to figure it out potential sequence biases upon the modification. The modified protoc…
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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 befor…
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Hi Kai,
Here is a quick question about peak calling. After having a detail look with the export.rs code, I understanding you prefer to evoke macs2 with '--call-summits'. This is not the same wit…
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Hello,
I have been trying to train a model with ChromBPnet. I created my own training bias model and I have a few questions for two topics:
1) Training Bias Model
After training my custome bi…
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For new term requests, please provide the following information:
## Preferred term label
sci-ATAC-seq3
## Synonyms
none _(although, possibly Sci-ATAC-seq3 if we want to correspond with sci…
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Hi! I am trying to use your ATAC-seqs produced in your article "De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes". I noticed that you uploaded the narrowpeak file to…
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Hi, msbentson,
I encountered some problems when using the PlotAggregate command. I obtained the binding pattern of Stat2 from three separate BINDetect results and wanted to visualize the difference…
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Is the "TOBIAS ATACorrect" suitable for DNase-seq where DNase I cut the chromatin?