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Depends on proper barcode information in fastq file names.
https://github.com/nathankw/pulsar_lims/issues/90
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Hi,
I am trying to use chromVAR package with 10x public dataset. I want to use the fragments.tsv files but it is a very large file and it always runs out of memory. I am using R on a cluster with m…
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Hello,
I am wondering whether there is a straightforward way to use AMULET with the output of scATAC-pro. The vignettes seem to require the outputs from cellranger which conveniently produce a csv…
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I'm trying to use ChromVAR to read in output from the 10X cellranger-atac pipeline. I believe I have it working when reading in the peak_bc_matrix as my own count table, but I'd also like to use chrom…
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Hi there,
Thanks so much for creating this package. I'm in the processing for trying it for one of my samples.
I have bulk WGS and 10x scATACseq (also paired scRNAseq; outputs generated by cellrange…
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Hello! I've been trying to use your software, but I only ever see global CNV changes - no hint of single cell changes.
I've tried changing the windows size between 1e5, 5e5, and 1e6, the minFrags …
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I've successfully run the example. I don't understand the output
out/merged_snp/jurkat_chr1/final.tsv.gz
What is the final call? And is what should I use as the measure of confidence?
Thank…
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Hello,
I am getting the following error when running the function.
```
Assuming paired scATAC/scRNA-seq data ..
Matrix object input detectedCentering counts for cells sequentially in groups of …
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**Describe the bug**
Hello, I'm trying to run SCENIC+ using SnakeMake in a linux machine (centos 9), on the tutorial dataset.
I ran scATAC-seq preprocessing in python (using pycistopic, using the tu…