search

spcdot / CopyscAT

Inferring CNV data from single cell ATAC seq
GNU General Public License v3.0
22 stars 6 forks source link

differing number of bins for reference and sample #30

Open Thienni-creator opened 1 year ago

Thienni-creator commented 1 year ago

Hi thanks for creating this tool, I have the problem that the input file processed by process_fragment_file.py and the references either provided by you and also the ones created with your "generateReferences"-function have differing number of bins in chromosome 1. I have already removed all excess and alt-chromosomes and due to that the collapseChrom3N function can't perform mutate due to the differing numbers

LoYo-81 commented 10 months ago

hello, I have encountered the same problem as you.How did you solve it?

Thienni-creator commented 10 months ago

I haven't yet managed to solve it, I switched to using RIDDLER and epiAneufinder for the purpose of CNV detection based on ATAC-seq data

dzhao98 commented 10 months ago

Hi So I had a similar problem. I removed alternative/scaffold, add back the header then run the process fragment. I realized I made a mistake of using a wrong cytoband file with the wrong binsize when initialzing the environment. It solved for me I do not know if you have similar problems