run_sgrna_quant fails

[AMChalkie]

Hi,

I see the following error:

Error in data.frame(sgRNA = quant_ret$sgRNA, sequence = quant_ret$sequence) : arguments imply differing number of rows: 79633, 79637

traceback() 3: stop(gettextf("arguments imply differing number of rows: %s", paste(unique(nrows), collapse = ", ")), domain = NA) 2: data.frame(sgRNA = quant_ret$sgRNA, sequence = quant_ret$sequence) 1: run_sgrna_quant(LIBRARY_FASTA, df_design)

Suggest adding a more robust check in the output section. Cheers Alistair

[AMChalkie]

When running run_sgrna_quant(FASTA, df_design, sg2gene) I see this comment: 4 sgRNA sequences were repetitive and will be discarded.

Final Mappability: 88.2023% Parsed with column specification: cols( PZP_1 = col_character(), PZP = col_character() ) Error: by can't contain join column id which is missing from LHS Run rlang::last_error() to see where the error occurred.

rlang::last_error() <error/rlang_error> by can't contain join column id which is missing from LHS Backtrace:

1. CB2::run_sgrna_quant(...)
2. dplyr:::left_join.tbl_df(df_map, df_count, by = "id")
3. dplyr:::common_by.character(by, x, y)
4. dplyr:::common_by.list(by, x, y)
5. dplyr:::bad_args(...)
6. dplyr:::glubort(fmt_args(args), ..., .envir = .envir) Run rlang::last_trace() to see the full context.

When running: (with duplicates) run_sgrna_quant(FASTA, df_design)

run_sgrna_quant(FASTA, df_design)

I get Error in data.frame(sgRNA = quant_ret$sgRNA, sequence = quant_ret$sequence) : arguments imply differing number of rows: 79633, 79637

traceback() 3: stop(gettextf("arguments imply differing number of rows: %s", paste(unique(nrows), collapse = ", ")), domain = NA) 2: data.frame(sgRNA = quant_ret$sgRNA, sequence = quant_ret$sequence) 1: run_sgrna_quant(LIBRARY_FASTA, df_design)

[hyunhwan-jeong]

Hi, can you share your fasta file?

Thank you,

Hyun-Hwan Jeong

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When running run_sgrna_quant(FASTA, df_design, sg2gene) I see this comment: 4 sgRNA sequences were repetitive and will be discarded.

Final Mappability: 88.2023% Parsed with column specification: cols( PZP_1 = col_character(), PZP = col_character() ) Error: by can't contain join column id which is missing from LHS Run rlang::last_error() to see where the error occurred.

rlang::last_error() <error/rlang_error> by can't contain join column id which is missing from LHS Backtrace:

1. CB2::run_sgrna_quant(...)
2. dplyr:::left_join.tbl_df(df_map, df_count, by = "id")
3. dplyr:::common_by.character(by, x, y)
4. dplyr:::common_by.list(by, x, y)
5. dplyr:::bad_args(...)
6. dplyr:::glubort(fmt_args(args), ..., .envir = .envir) Run rlang::last_trace() to see the full context.

When running: (with duplicates) run_sgrna_quant(FASTA, df_design)

run_sgrna_quant(FASTA, df_design)

I get Error in data.frame(sgRNA = quant_ret$sgRNA, sequence = quant_ret$sequence) : arguments imply differing number of rows: 79633, 79637

traceback() 3: stop(gettextf("arguments imply differing number of rows: %s", paste(unique(nrows), collapse = ", ")), domain = NA) 2: data.frame(sgRNA = quant_ret$sgRNA, sequence = quant_ret$sequence) 1: run_sgrna_quant(LIBRARY_FASTA, df_design)

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[AMChalkie]

Here you go: broadgpp_brie_crispr_library.fasta.gz