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Hello,
Can you add a tutorial on how to generate `pancreas_multiome_2022_processed_atac.h5ad` to the existing tutorial 'Mouse Pancreatic Endocrinogenesis (scATAC-seq) | Training with an RNA-Dynami…
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## Hierarchy of RE
```
LTR (Family) —> L1 (Sub-Family) —> L1_Rod (Gene) —> L1_Rod_dup1 (Transcript)
LTR (Family) —> L1 (Sub-Family) —> L1_Rod (Gene) —> L1_Rod_dup2 (Transcript)
LTR (Family) —> L1 …
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In [ATAC-seq/auyar/](https://github.com/TheJacksonLaboratory/ATAC-seq/tree/master/auyar), there are a number of bash shell scripts (`*.sh`) that need to be unified with the workflow described by auyar…
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Hi AMULET team,
I have a 10X multiome kit dataset and trying to run AMULET on the ATAC data.
The fragments input file is the same, but the singlecell.csv is no longer available as CellRanger outpu…
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Hi,
Sorry it might be a naive question, but I cannot find a way to overcome it...
I am trying to install your pipeline. I think I have installed all required database/softwares, however, I got the f…
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I tried to run the pipeline but as a new user, I got some difficulties. I have 8 fastq files and tried to make the files necessary to run the pipeline.
## **OS/Platform**
- OS/Platform: SCG cluste…
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### Description of the bug
Currently, the IGV reporting directory tries to keep all the resource files within it to make the directory self-contained. It does so through the `includeInputs` mechanism…
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Hi, @bnprks. I followed the [BPCells tutorials](https://bnprks.github.io/BPCells/articles/pbmc3k.html#atac-normalization-pca-and-umap) but computed SVD using `svds()` instead of `irlba()`. For example…
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```
❯ docker run --rm\
-v /mnt/nvme-1/2-hubmap/spatial/ref-scrna/data/ft:/app/data\
-v /mnt/nvme-1/2-hubmap/spatial/ref-scrna/out/ft:/app/out\
-v /mnt/nvme-1/2-hubmap/sc-transmogrifier:/app/sc-…
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I have bulk ATAC-seq from two cell populations (two replicates each). Papers suggest for bulk counts to apply quantile normalization followed by GC bias normalization using CQN.
Does chromVAR acco…