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Hi Rongxin,
SnapATAC is an awesome package for single cell ATAC-seq analysis. After peak calling by MACS2, I am wondering how can I generate the bdg or bigwig file of a subset of nuclei based on co…
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Hello,
I have been trying to figure out how to incorporate external spike-in normalisation factors to both single-end and paired-end ChIP-seq data for peak calling with MACS2.
I tried peak calli…
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The doc command blocks aren't copy-and-pasteable due to extraneous `$` symbols, e.g.
To run locally, we invoke the following command:
```
$ bdg-deca \
$ --targets \
$ --samples \
$ --o…
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### Context
I added the `bdg-link-` badge to the Sphinx project.
### Proposal
I need a tooltip for a badge. The tooltip will be displayed when the user hovers over the badge. For example, the toolt…
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Very strange behavior. I have four ATAC-seq samples across two experimental conditions (two each). For three of the samples, Genrich identifies ~10-30k peaks, but for the other one, it identifies 0. H…
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I have a few questions regarding the parameters used in the dynamic program:
1. For each block, it appears that you solve `nb_bdg_all * nb_bdg_abar` optimization problems, the former imposing an ov…
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Hi,
I hope this message finds you well. I'm reaching out to seek your assistance regarding an error I encountered while using Circlehunter to identify extrachromosomal DNA (ecDNA) in my ATAC-seq da…
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Use the ADVANCE & MONICA to ADAM mapping spreadsheet to create the avro file
Depends on #14.
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Hello, the bdg file generated by `bdgcmp ` can convert into a bigwig file, for a particular region, what is the relationship between the signal values I get with bigwig and the reads count I get with …
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Hi,
I have a number of atacseq bams and their total read numbers differ. I did peak calling with and without --SPMR and there is no difference between the two ......broad_peaks.broadPeak files. yet t…