Mohammad Izadi

Hi @SeppeDeWinter, Many Thanks for your response. I attached my fragments file in this comment. Thanks again for your help. Best, Mohammad [fragments.tsv.gz](https://github.com/aertslab/scenicplus/files/12600409/fragments.tsv.gz)

Hi @SeppeDeWinter Thanks for your response. I attached wrong fragments file and I upload it again. I convert anndata to fragments.tsv file and now I delete rows that have zero...

Hi @SeppeDeWinter, Thanks for your helping. I have similar issue and I can't get output files in "pseudobulk_bed_files" and "pseudobulk_bw_files" dir. Can you help me to solve this? Best, Mahan