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error for export_pseudobulk #314
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The function This can be caused when the function is not able to match cell barcodes between your The reason for this is probably because you appended sample ids to the barcodes in your fragments file ("500_" for example). It's not necessary to merge your fragment files before running pycistopic/SCENIC+. You can just specify multiple files in your Also could you show the head of All the best, Seppe |
Thank you very much for your reply,but I still haven't solved the problem, I tried without merging and just inputting one fragments file, It still reports the error. Also I checked the cell barcodes between my cell_data dataframe and the fragments file , and didn't find any difference between them. I added "_n" (for example "_1") at the end of the barcodes to distinguish different sample sources. This is one of my fragment files:
And head of cell_data:
Thanks again for your help and Wish you all the best. ayong |
Hi Ayong Can you try without adding the "_n", cistopic will automatically append sample ids to your cell barcodes. All the best, Seppe |
HI HI Seppe Your guidance helped me find an idea. This problem has been solved. And because the data sources are different,there are a lot of duplications in their barcodes .So I added my own tags. There are cores to solving the problem: Such as:
Thanks for your help and Wish you all the best. Ayong |
Great to hear that your issue is solved. I wish you all the best as well and good luck with your analyses. I'm closing this issue now feel free to open new ones. Seppe |
#Describe the bug
When I apply my data to export_pseudobulk function of SCENIC+ pipeline,I meet error.
I don't know where this file(ADM.fragments.tsv.gz ) came from ,I have never imported this file.
#Code
#Error output
raise ValueError(f"Fragment file {path_to_fragment_file} does not exist.")
ValueError: Fragment file /public/home/chenxy/data/Synapse/scenicplus/00_data.import/ray_spill/pancan/ADM.fragments.tsv.gz does not exist.
#Additional context
This fragments file is created by merging multiple fragments files. I refer to this process
#Version (please complete the following information):**
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