Start j_alignment with the portion after the Cys
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@ -126,7 +126,7 @@ get_hvr_sequences <- function(sequences, vdj_segments, cores = detectCores()) {
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)
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cys_coordinates <- parallel::mclapply(v_alignment, FUN = get_cys_coordinates)
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cys_coordinates <- parallel::mclapply(v_alignment, FUN = get_cys_coordinates)
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cys_df <- as.data.frame(do.call(rbind, cys_coordinates))
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cys_df <- as.data.frame(do.call(rbind, cys_coordinates))
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remaining <- Biostrings::subseq(sequences, start = unlist(cys_df$end))
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remaining <- Biostrings::subseq(sequences, start = unlist(cys_df$end) + 1)
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j_alignment <- parallel::mcmapply(remaining,
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j_alignment <- parallel::mcmapply(remaining,
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df$j_seq,
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df$j_seq,
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FUN = align_sequence,
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FUN = align_sequence,
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