NucleoATAC
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GreenleafLab
nucleosome calling using ATAC-seq
Based on #95 but with a few small fixes, updated setup.py, and an added test case.
Hello. I'm hoping someone might see this and be able to help me out! I'm running pyatac ins which seems to run just fine with no errors, however my output...
Hi, As I am becoming more familiar with NucleoATAC, I am realizing you do not have a way to set a normalization factor, how would you suggest doing that? I...
Hi Alicia, I am trying to use MNase data to test nucleoatac. I have a question regarding to the prediction for nucleosome. So I found that many of the high...
Hi!@AliciaSchep, I simply want to get nucleosome position from MNase-seq data using NucleoATAC. But I don't understand 3rd Necessary Files: 3) Sorted bed file with regions for which nucleosome analysis...
Hi, I have come across NucleoATAC recently and in order to test the package, I was going to use the same data that was published for S. cerevisiae in 2015....
Thanks for making this great library! What's the maintainence status though? Is any fork getting updated at all?
Hi, I have been using your excellent NucleoATAC tool, but I wanted to check I have been using the output correctly. I need to assess nucleosome occupancy between different samples....
Dear Alicia, Thank you for developing the method and package. I have some basic questions and confusion about terminology. *.nucmap_combined.bed.gz - This file contains regions that are bound by chromatin...
Hi @AliciaSchep , I'm new to ATAC-seq, i wonder how did you get the following heatmap, Is there any software that can do the job ? i tried deeptools, but...
