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Hoohm / CITE-seq-Count

A tool that allows to get UMI counts from a single cell protein assay
https://hoohm.github.io/CITE-seq-Count/
MIT License
79 stars 44 forks source link

barcode bug #152

Open craigamartens opened 3 years ago

craigamartens commented 3 years ago

Hi, I have 2 issues, one is when setting the estimated cell number, CITE-seq-Count appears to force the cell count to that number. I am worried this can lead to inaccurate/biased results. For example, if I set cell number to 8000, I get 8000 +/- 10 cells back, if I set the same dataset to 10,000, I get ~10,000 back. To try to avoid this, I tried to set the cell barcode mismatch to 0 and then got the following error.

Correcting cell barcodes Looking for a whitelist Collapsing cell barcodes Traceback (most recent call last): File "/home/martensc/.local/bin/CITE-seq-Count", line 11, in load_entry_point('CITE-seq-Count==1.4.4', 'console_scripts', 'CITE-seq-Count')() File "/home/martensc/.local/lib/python3.6/site-packages/cite_seq_count/main.py", line 394, in main ab_map=ordered_tags_map) File "/home/martensc/.local/lib/python3.6/site-packages/cite_seq_count/processing.py", line 368, in correct_cells ab_map=ab_map, File "/home/martensc/.local/lib/python3.6/site-packages/cite_seq_count/processing.py", line 312, in collapse_cells for real_barcode in true_to_false: TypeError: 'NoneType' object is not iterable

All I did was to add the following to my command, which works fine otherwise: --bc_collapsing_dist 0 Thanks, Craig

Hoohm commented 3 years ago

Hello @craigamartens,

Thank you for pointing it out, I'll add it to my long list of fixes for 1.5.0 :)