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Hello,
currently, I am processing a multimodal (ScRNA- and scATAC-seq) single nuclei dataset using Signac. Because I have a problem with MACS2 installation in the Anaconda prompt on the Windows PC …
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Hello, I am trying to read in multiomic data from the newly released 10X open source datasets: https://www.10xgenomics.com/resources/datasets/multiomic-integration-neuroscience-application-note-vi…
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Hi,
Very impressive work with well documentation and ease of use. Even though this software is mainly aimed for ATAC-seq, this software may be also suitable for MNase-seq based assays? In your ATACor…
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Hi,
I have a 10x multiomics (RNA+ATAC) experiment, and am trying to use `chromap` for the ATAC portion and associate it with RNA analyzed by `alevin-fry`. My ATAC files are in the format with `R1`, `…
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Thank you.
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https://mp.weixin.qq.com/s/06qiP4_yE8UOvXt4eP6org
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**Describe the bug**
Execution failed while running `mgatk tenx` mode. I keep having an issue in the process_one_slice rule which occurs only for one .bam. More specifically, samtools fails to gene…
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I set the absolute path for the bam files to feed `--density`. But the problem is that the bash command line version always take it as the relative path by default. It always add the current working f…
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I'm trying to run gimme maelstrom but it gets stuck here:
2020-02-13 10:25:29,036 - INFO - Starting maelstrom
2020-02-13 10:25:29,066 - INFO - motif scanning (counts)
2020-02-13 10:25:29,067 - IN…
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Dear Tim,
An error occured with `CreateChromatinAssay` and `seqlevels` when I was trying out the vignette on SNARE-seq. I was wondering whether there's any setting issues? (good with vignette on 10x…