snap.tl.macs3

[TingTingShao]

Hi,

When I ran the step snap.tl.macs3, the return dictionary is None, could I please ask the reason behind this?

I also called peaks in pycistopic, it returned the value, when setting the same parameter with snapatac2.

Code

narrow_peaks_dict=snap.tl.macs3(adat, groupby=config['leiden_mnc_resolution'], 
    replicate='sample', 
    qvalue=0.05,
    shift=73,
    extsize=146,
    # key_added='macs',
    tempdir=config['tmp_dir']
    )

pycistopics

narrow_peaks_dict = peak_calling(config['macs_path'],
                                bed_paths,
                                config['macs_file'],
                                genome_size='hs',
                                n_cpu=1,
                                input_format='BEDPE',
                                shift=73,
                                ext_size=146,
                                keep_dup = 'all', # Whether to keep duplicate tags at te exact same location.
                                q_value = 0.05,
                                _temp_dir = os.path.join(config["tmp_dir"], 'ray_spill')
                                )   

Thanks, tingting

[beyondpie]

Hi @TingTingShao

1. The input adapt is the SnapATAC2's AnnData ?
2. What's the output of onfig['leiden_mnc_resolution']? If it's string, does it exist in adat.obs and indeed there are cells in that group?

I think the information you provide is not enough for us to help you check what happened.