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Hello,
I've got a question. I would like to try your software to perform peak calling, but instead of using Chip-seq data I woul like to use it on ATAC-seq data.
Do you think it is possible? If so,…
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Hi,
I have a question of using scGPT on ATAC data. The typical scATAC-seq has binarized values 0 and 1, so how to make the ATAC counts as bins? Should we only make the counts to only 2 bins: 0-bin an…
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Dear Team,
I calculated partition heritability for ATAC seq peaks by using 106 GWAS sumstats.
For example: for "PASS.Schizophrenia.Trubetskoy2022 GWAS sumstats", I have 98 categories for peaks. I …
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Hi kai,
When using Taiji, I encountered some issues while using a YAML file as input. The error message I encountered is:
there is my input.yml:
```python
RNA-seq:
- id: RNA_NIP_0h
…
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Hi !
I am trying tu use msCENTIPEDE to generate TF footprints for several ATAC-seq data sets i've produced.
I wanted to have general advices on how to achieve the most accurate workflow.
So far, w…
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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…
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Hi, when I check the pepatac log, I find this command: `bedtools intersect -a /data3/01.projects/GROUP01043/10.ATAC_seq_test/poj5/pepatac/mas1/peak_calling_mm10/mas1_peaks_normalized.narrowPeak -b /da…
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#8
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Hi,
I have some some bulk ATAC and RNA seq in which I wanted to identify some DORCs. Is it possible to use the dorc function in this kind os data (ie importing my bulk rds into the objects)? Of cour…
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Hallo, I wanna ask if its possible for you to upload the code used for data-integration of ATAC-sequencing data with LIGER :)