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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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recently seen: ATAC-Seq_m. - I assume this should be ATAC-Seq_mouse
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Hi there, this is a bit of a shot in the dark, but I'm trying to wrap my head around analyzing broadPeak chip-seq files and stumbled across this repo. The approach described in https://github.com/resk…
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Thank you very much for developing the excellent ATAC-seq package.
I'm encountering an issue with the part “Running footprinting scores”. I'm following your tutorial and using my own single-cell RNA…
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Hi,
I am currently running an ATAC-seq dataset with 16 samples (with plans to expand in the future). The dataset involves two conditions, four treatments, and two replicates per treatment, and I w…
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Hi everyone. Great work for the new paper. I'm trying to replicate the results in your joint ATAC-seq and RNA-seq paper. I saw that for the analysis of A549 ATAC-seq, you mention that the procedure wa…
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Hello,
I was wondering if TEpeaks would work for ATAC-seq peaks? Have you ever tried it?
Thank you
Rita
RRebo updated
8 months ago
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Hi,
Thanks for this pipeline.
I was trying to use it on atac-seq data. I got the following error message:
`Caused by: Process bamCoverage (1) terminated with an error exit status (127) Comma…
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# About
Let's rename the `Input` column to `Input_Control` and make it an optional column (for ATAC-seq). The name `Input` for ChIP samples could causes some confusion for users who are not experie…
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Hello,
Thanks for this very useful package!
I just have a few questions after runnning on single-cell ATAC-Seq libraries generated from the 10X multiome kit. I ran using the following commands:
…