seasoncloud

Hello! Thanks for your interest in Alleloscope! I just uploaded the centromere and telomere data for hg19 to the "data" folder. The data were downloaded from the UCSC Table Browser...

Hello, I checked the mission bio website and saw this page: https://support.missionbio.com/hc/en-us/articles/360045939853-Pipeline-output-files-overview Not sure if you got output files the same as those listed here. There is a file "barcode.cell.coverage.tsv"....

Hi, I also have problem installing SCIPhI at the compiling step. Could you please provide additional instructions for installation? Thanks!

Hello! Sorry for the late reply!! Please see the following answers-- 1. The bin-widths do not need to be fixed. The output from the 10x scDNA-seq preprocessing may already include...

Hello, sorry for the later response and thanks for your interest in Alleloscope! Currently, we only tested Alleloscope's performance using an unbiased segmentation from either matched WGS/WES data or any...

Hello, thanks for you interest in Alleloscope! I think it is the problem for plotting. One possibility is that your alt_all/ref_all/var_all files have the SNPs not on chr1-22. Could you...

Yeah possibly. I think the table function I used in this helper function cannot handle this large file. I just checked the barcode files. There are 731466 barcodes. I typically...

Hello, Yes I would suggest using the filtered barcodes since many of the barcodes in the raw data are not real cells. As far as I know, most copy number...

I see. Yeah I think you could try using this public control dataset. An example for the scDNA-seq cell line dataset can be found [here](https://github.com/seasoncloud/Alleloscope/tree/main/samples/SNU601/scDNA). This should be similar for...

Hello, You could try removing the "mincell = 100" setting when running the Genotype_value function (to exclude regions which too fews cells have reads covering) to see if it solves...