Splicing Neo Antigen Finder (SNAF) is an easy-to-use Python package to identify splicing-derived tumor neoantigens from RNA sequencing data, it further leverages both deep learning and hierarchical Bayesian models to prioritize certain candidates for experimental validation
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slight discrepancies of junction frequency between freq0 file and B antigen result #28
It has been brought to my attention that, the junction frequency reported in frequency_stage0_verbosity1_uid_gene_symbol_coord_mean_mle.txt is not always the same as reported in B antigen results.
The reason behind that is, the n_sample reported in frequency_stage0_verbosity1_uid_gene_symbol_coord_mean_mle.txt considers the tumor specificity threshold (n_tumor - n_control > 20 reads) while cohort_frequency reported in B antigen results simply counts the non-zero entries in the data frame, which will result in slightly higher frequency in B antigen results.
Just want to put it out here in case you encounter this!
It has been brought to my attention that, the junction frequency reported in
frequency_stage0_verbosity1_uid_gene_symbol_coord_mean_mle.txtis not always the same as reported in B antigen results.The reason behind that is, the
n_samplereported infrequency_stage0_verbosity1_uid_gene_symbol_coord_mean_mle.txtconsiders the tumor specificity threshold (n_tumor - n_control > 20 reads) whilecohort_frequencyreported in B antigen results simply counts the non-zero entries in the data frame, which will result in slightly higher frequency in B antigen results.Just want to put it out here in case you encounter this!
Best, Frank