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hello,
Thank you for this package! Is there a way to extract the original cells for both the RNA and ATAC-seq that were used to make the pseudomultiome and map those to the cells for the output mat…
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Hi,
Thank for your practical tool!
I am working on single cell ATAC-seq data and I would like to classify the cells based on their cell types. It seems the only single cell ATAC seq dataset with g…
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Hello RGT-HINT,
I met error messages when running RGT-HINT footprinting:
```linux
rgt-hint footprinting --organism mm10 --paired-end --output-location /mnt/e/HYJ/2022_7_23_ATAC-seq/results/RGT_HINT…
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Thank you for your reply before.
Now I can successfully use snakemake, and I have prepared all input files and softwares required for snakemake. I have made the config.yaml and put it in the folder "…
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Can this platform be used for shallow scATAC-seq data? I have output from cellranger atac count pipeline. How can I generate doubletD inputs from this?
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Hi @leepc12 , first, thank you for the great pipeline here 🙏
## **Describe the bug**
The failure is partially due to my input fastqs having identical file name and differs as different file on pa…
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By genomic features I mean: transcript exons, whole region, transcription start sites etc.
This would be useful for looking at chromatin availability at a TSS, as is commonly done with ATAC-seq ana…
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Dear Jimin, Your research has been very helpful in my work!
I am trying to reproduce the best results of your method as our baseline to compare.
Does Origami provide pre trained models for other ce…
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**Describe the bug**
We run the following command for ATAC sample:
> mgatk tenx -i cellranger/ATAC-SC05/possorted_bam.bam -n ATAC-SC05 -o ATAC_mgatk/ATAC-SC05 -c 32 -bt CB -b cellranger/ATAC-SC…
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How many cell types are required for haystack_bio to provide accurate and reliable results? For example, I have ATAC-seq and RNA-seq data on three cell types? Would this be sufficient for running ha…