-
Hi,
Have you tested if the model can be trained to infer DNase-seq signal from ATAC-seq?
Best,
Chang
-
Is there a way to run PePr without specifying input files, as is the case for analyzing ATAC-seq/DNase-seq data?
-
(I received this question by email, and am including it and the response below - jmg)
I read your work on improved peak calling with MACS2. I belong in the
worst category and have been running MAC…
jsh58 updated
5 years ago
-
Dear developers,
I wonder if there is documentation/example for training based on Dnase/ATAC-seq input? I would highly appreciate suggestions on parameter tweaking!!
It seems ATAC/Dnase are supp…
-
1. [Integrating ChIP-seq with other functional genomics data](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5888983/pdf/ely002.pdf)
2. [2014-nature review-Identifying and mitigating bias in next-gener…
-
- [x] Remove "(beta)" from title of track hub
- [x] Change "general cCREs" to "Cell-type Agnostic cCREs" and this should always appear as the first "folder" of the track hub display
- [ ] For select…
-
Hi! I have tried to train the Leopard model only on the DNA seq of reference genome and remove the DNase-seq / delta DNase out from the input feature. However, the prediction result only gives the val…
-
https://github.com/r3fang/SnapATAC/blob/c3ab177558f0fe9c47cbd68969df7b06de5b07d9/R/runMACS.R#L32
According to the [MACS2 page](https://github.com/taoliu/MACS) the settings
```--shift -100 --extsi…
-
您好！你们的论文非常棒，我尝试重新训练一次模型，后面我打算用自己的新HIC数据复现一遍。
我从当前github代码库能够通过数据处理的代码到6种细胞系类型的序列数据Seq.npz，但是无法获得这6种细胞系数据对应的DNase数据。
于是我重新阅读文章，从补充文件种得到一个Excel表格，里面的子表1提到配套的DNase数据，但是似乎与您提供的“demo”目录中“DNase”数据不太一样…
-
Remove the "SELEX", "WGS", and the empty artifact. Check how many records are in SELEX and WGS first before removing and post this info here (with a date/timestamp when you retrieved these record…