Wenbao Yu
Wenbao Yu
I guess probably you're using an old version of configure_user.txt file. Do you define Top_Variable_Features in you configure file? If not, can you add a line like Top_Variable_Features = 5000...
Can you increase it to a bigger value like 0.2? Because I had internally filtered some rare peaks (like open in less than 1% of cells) from the variable features,...
@aseyedia is that the issue? Thanks.
yes, `integrate` is just a wrapper.
Can you check some intermediate results? Such as how many cells did you get under filtered_Matrix folder or any other output? I guess some of your filtering parameters may be...
No, you need to decrease your thresholds, for instance, min_uniq_frags to 2000, min_frac_peak 0.25. You can increase max_frac_mito to 0.15 or 0.2.
The *clustering* module is not included in the process module by design. You need to run *clustering* or *downstream_analysis* before running the report module.
Oh, I see. Not sure what's going on, I will double check the signularity version. Does other clustering method work?
Not sure what exactly happened. Have you checked the outputs? I guess you probably ended up too few number of cells.
group1 = one group2 = rest should work for this purpose.