Monopogen
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KChen-lab
SNV calling from single cell sequencing
Good morning, Thank you very much for the help provided previously. I am trying to use the output derived from the somatic module, i.e. chr.SNV_mat.RDS in the openCRAVAT software but...
Hello! Im having a bit of difficulty generating the bam.lst file that will be used for data preprocessing. I had made my bam.lst file containing the paths to the bam...
Hi, I'm encountering an error during the final step of the SNV calling tutorial for scRNA-Seq data. Specifically, I get: ``` [2024-05-21 17:09:53,243] INFO Monopogen.py Run LD refinement ... Rscript...
We are following the example here and noticed the following overlap with the example data between somatic SNV calls made from scRNAseq with v1.0 and v1.6.  Are you surprised...
We are particularly interested in calculating SNP (Single Nucleotide Polymorphism) expression levels using single-cell ATAC data. We have utilized the Monopogen tool to compute genotypes associated with germline mutations. However,...
I'm using the example data from the documentation. In v1.6.0 - the file `chr20.germline.vcf` does not get generated from the germline calling step. ``` ${path}/src/Monopogen.py germline -a ${path}/apps -r region.lst...
Hello! I am writing to ask you if you could list me what the outputs of each of the three somatic modules should be. In fact, after the cellscan module...
HI! I'm having a problem with the cellScann module, in particular I can't understand the reason for this error: INFO Monopogen.py Get single cell level information from sequencing data... INFO:__main__:Get...
Hi, I have been running preprocess step and then germline snv calling on my Mac. However, all my outputs in .gl.vcf.gz have zero bytes. Are there any errors? Would the...
Hi, Thanks so much for developing this tool! I've been trying to get the test dataset running to call somatic mutations, but have been having some trouble. I downloaded the...
