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Hi @nezirajt, are you working on mouse data? Can you provide me with some more descriptions like what does the logs show? |
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Thanks for your quick reply! I am working on human data, and as it seems when reassigning alleles those contigs that fail during the "creating germline" step are removed:
null device PROGRESS> 21:00:06 |####################| 100% (3,280) 0.0 min OUTPUT> test_y_heavy_igblast_db-pass_genotyped_germ-pass.tsv For example in this case 41. If I merge the "/dandelion/tmp/filtered_contig_igblast_db-pass.tsv" files (so before performing these steps) vs. "/dandelion/filtered_contig_dandelion.tsv" (after performing these steps), in the second case I will have less of contigs in total. Do I have to specify the human gremline reference in this step: ddl.pp.reassign_alleles(Sample, combined_folder="test")? Thanks a lot! |
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Hi, I have been using dandelion for BCR analysis. I noticed that after performing pre-processing (including reassign alleles and isotypes), the total number of contigs is reduced when merging the output filtered_contig_dandelion.tsv files. Will contigs be removed during these steps? Thanks a lot!
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