rcorces
commented
2 years ago Hi @artgolden! Thanks for using ArchR! I am currently on paternity leave and will not be responding to any issues or discussion threads. I plan to be back in late January and will do my best to address your issue then.
In the meantime, it is worth noting that there are very few actual bugs in ArchR. If you are getting an error, it is probably something specific to your dataset, usage, or computational environment. Search the previous Issues, Discussions, function definitions, or the ArchR manual and you will likely find the answers you are looking for.
If you are able to solve your issue, please post the solution and close this issue post.
Otherwise if you would like my help when I return, you must respond to the following questions unless your original post already contained this information:
1. If you've encountered an error, have you already searched previous Issues to make sure that this hasn't already been solved?
2. Can you recapitulate your error using the tutorial code and dataset? If so, provide a reproducible example.
3. Did you post your log file? If not, add it now.
yaxiliu-1996
cnluzon
Describe the bug
Error in FUN(X[[i]], ...) : cell_id not in colnames of 10X singlecell.csv file! Are you sure inut is correct?Cellranger-atac in version 2.0.0 has changed the format of theirsinglecell.csvfiles and there is no cell_id column anymore. Instead there is a boolean column is__cell_barcode. singlecell_example.csvTo Reproduce Run
getValidBarcodes()function with 10Xsinglecell.csvgenerated with Cellranger-atac version >2.0.0.Expected behavior Correctly load cell-barcodes that have passed cellranger-atac filteres.
Session Info R version 4.1.1 (2021-08-10) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 20.04.2 LTS
Matrix products: default BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.8.so
locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=C
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages: [1] BSgenome.Mmusculus.UCSC.mm10_1.4.3 BSgenome_1.62.0
[3] rtracklayer_1.54.0 Biostrings_2.62.0
[5] XVector_0.34.0 forcats_0.5.1
[7] stringr_1.4.0 dplyr_1.0.7
[9] purrr_0.3.4 readr_2.1.1
[11] tidyr_1.1.4 tibble_3.1.6
[13] tidyverse_1.3.1 patchwork_1.1.1
[15] ArchR_1.0.2 magrittr_2.0.1
[17] rhdf5_2.38.0 Matrix_1.3-4
[19] data.table_1.14.2 SummarizedExperiment_1.24.0
[21] Biobase_2.54.0 GenomicRanges_1.46.1
[23] GenomeInfoDb_1.30.0 IRanges_2.28.0
[25] S4Vectors_0.32.3 BiocGenerics_0.40.0
[27] MatrixGenerics_1.6.0 matrixStats_0.61.0
[29] ggplot2_3.3.5
loaded via a namespace (and not attached): [1] bitops_1.0-7 fs_1.5.1 bit64_4.0.5
[4] lubridate_1.7.10 httr_1.4.2 rprojroot_2.0.2
[7] tools_4.1.1 backports_1.2.1 bslib_0.3.1
[10] utf8_1.2.2 R6_2.5.1 DBI_1.1.1
[13] colorspace_2.0-2 rhdf5filters_1.6.0 withr_2.4.3
[16] tidyselect_1.1.1 bit_4.0.4 compiler_4.1.1
[19] cli_3.1.0 rvest_1.0.1 Cairo_1.5-12.2
[22] xml2_1.3.2 DelayedArray_0.20.0 sass_0.4.0
[25] scales_1.1.1 Rsamtools_2.10.0 digest_0.6.29
[28] rmarkdown_2.10 pkgconfig_2.0.3 htmltools_0.5.2
[31] dbplyr_2.1.1 fastmap_1.1.0 rlang_0.4.12
[34] readxl_1.3.1 rstudioapi_0.13 BiocIO_1.4.0
[37] jquerylib_0.1.4 generics_0.1.1 jsonlite_1.7.2
[40] vroom_1.5.7 BiocParallel_1.28.2 RCurl_1.98-1.5
[43] GenomeInfoDbData_1.2.7 Rcpp_1.0.7 munsell_0.5.0
[46] Rhdf5lib_1.16.0 fansi_0.5.0 lifecycle_1.0.1
[49] stringi_1.7.6 yaml_2.2.1 zlibbioc_1.40.0
[52] grid_4.1.1 crayon_1.4.2 lattice_0.20-44
[55] haven_2.4.3 hms_1.1.1 knitr_1.33
[58] pillar_1.6.4 rjson_0.2.20 XML_3.99-0.8
[61] reprex_2.0.1 glue_1.5.1 evaluate_0.14
[64] modelr_0.1.8 vctrs_0.3.8 tzdb_0.2.0
[67] cellranger_1.1.0 gtable_0.3.0 assertthat_0.2.1
[70] xfun_0.25 broom_0.7.9 restfulr_0.0.13
[73] GenomicAlignments_1.30.0 ellipsis_0.3.2