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Hello,
I am using macs3 hmmratac mode for ATAC-Seq samples without control samples. I am getting 0 value for columns 13 through 15 in accessible peaks output. Is this related to no control samples?…
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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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Current proposal:
There are only two levels of topics, the main card, and tags within the card
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- Help (one for each project e.g., Scanpy, Muon, ...)
- Tags = project subpackage or releva…
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Hi Team
I am trying to check if the pipeline is free from errors and I ran the validate command from the folder where the.cwl file is. I am getting java error as mentioned below. Has it to do with…
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Hi,
I would like to ask you a question about the +4 and -5 shifts. It is important to shift the raw reads in the pre-processing step to account for the 9-bp duplication in ATAC-seq. I am confused as …
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## **Describe the bug**
A clear and concise description of what the problem is.
Thank you for the pipeline,however I am having issues with running the pipeline on an HPC with slurm and singularity.…
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Dear @wkopp
I'm trying to run scregseg on real bulk ATAC-seq data to have sample specific states following the tutorial for cluster collapsed tracks.
Does the model normalize the countmatix? or …
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Seqspec (https://github.com/IGVF/seqspec) is a machine-readable specification for libraries, a file format based on yaml, that enables sequence read annotation. The scope is broader than ours, includi…
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I see your proposed workaround for #907
However, I'd like to chime in on the how useful having the option to NOT merge such bins would be to an ATAC-Seq workflow which desires to compare read-cou…
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Hi,
The compute nodes on my institution's HPC do not have routes to external networks.
When trying to run the pipeline I get `OSError: Tunnel connection failed: 403 Forbidden` at the step when it ex…