run_sgrna_quant fails

[Alistair Chalk]

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

[Alistair Chalk]

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)

[Hyun-Hwan Jeong]

Hi, can you share your fasta file? Thank you, Hyun-Hwan Jeong Get Outlook for iOS<https://aka.ms/o0ukef>

…

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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) — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_LiuzLab_CB2_issues_3-3Femail-5Fsource-3Dnotifications-26email-5Ftoken-3DAEWSZ6GJH4S7RQFGL5TMTMDQVXHMBA5CNFSM4JR7GNIKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEFIAP6I-23issuecomment-2D558893049&d=DwMCaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=-lih8OIo66XtgJH6zqJrfg&m=RHCXZANc-m0hPjGVnfLPHbKL5nIgpV5VvD32eY-NgrA&s=EgrfmOGLNOcT2piUY8U00Oc78ZfJlPQcFWhMk-pFrcQ&e=>, or unsubscribe<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_AEWSZ6BT2WTOZHZGIWCD5DDQVXHMBANCNFSM4JR7GNIA&d=DwMCaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=-lih8OIo66XtgJH6zqJrfg&m=RHCXZANc-m0hPjGVnfLPHbKL5nIgpV5VvD32eY-NgrA&s=njkxOOVrUx_rKbBxo-RWhWRSI_N-AeofuWKiNGppxnA&e=>.

[Alistair Chalk]

Here you go:
broadgpp_brie_crispr_library.fasta.gz