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# General Notes
This repository serves as a mostly automated p…
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_QTL mapping_ is so far narrow synonym of _genetic mapping_ but is also applicable to other chromatin features such as histone modifications, chromatin accessibility, ...
_Solution 1:_ Leave as is …
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Hi,
Excuse me. I am doing a project about TAD boundaries using scm3C-seq data of brain tissue. I can't search your cell-type identification results. Can you send me clusters and cell-type identific…
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I think it would be good to include the results of this benchmarking paper in the ATAC-seq processing section. It does a quantitative comparison of various libraries in the ecosystem and compares them…
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editor preferred term: single-nuclei ATAC-seq
alternate terms: snATAC-seq
textual definition: Analysis of the transposase-accessible-chromatin in single nuclei isolated from frozen tissue samples th…
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Thanks for Chromap wihch is really really helpful especially when dealing with very big dataset.
But I found that Chromap miss some region when deal with Hetero Chromatin
As shown in the figure, the…
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I came across some abrupt terminations when I used Cicero for the following two tasks: 1) creating the CCAN (chromatin hubs) and 2) inferring gene expression. Specifically, the function `generate_ccan…
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The issue is that we don't currently index the input of GAF files as-is, rather they go through several layers of abstraction. By the time the information from the input file hits the index, the input…
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Hi，
When following the protocol `Kim, S.H. et al. (2023). Simultaneous Single-Cell Profiling of the Transcriptome and Accessible Chromatin Using SHARE-seq. In: Marinov, G.K., Greenleaf, W.J. (eds) Ch…
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It seems the scheduling code does not feed arguments to change the chromatin fraction through to job scheduling properly. When I enter the "--chain-generator-C 0.3" argument, I get a crash and the sim…