FAQs#
Experimental Design#
Q: I got scRNA-Seq data in loom/h5ad/others. How can I convert it to a format YASIM-scTCR supports?
A: If your format is supported by AnnData, you may convert it using
convert_anndatacommand.Q: Do YASIM-scTCR support raw FASTQ reads from manufacturers like 10xGenomics, etc?
A: No. The generated FASTQ files should be analyzed using standard pipelines on a cell-to-cell basis.
Reproducibility#
Q: We observed that other databases are also providing nucleotide and/or amino-acid sequences for TCR gene segments.
A: You are free to use TCR gene segments from IMGT GENEDB, UniProtKb-SWISSPROT, IgBLAST Reference TCR. However, since our data is primarily based on CellRanger statistics, we still recommend you to use the same version of TCR segments used by us (i.e., Ensembl release 97). Using a different version of TCR segments will lead to the risk of:
Different nomenclatures. The IMGT reference may include
/in their gene names, which must be removed before further processing.Divergent sequences. The IMGT, SwissProt and Ensembl release 97 have different nucleotide and amino-acid sequences for the same TCR gene segment. IMGT VQUEST may include multiple sequences from different databases for the same gene.
Q: What’s the version of software used in your studies?
A: See the following table:
Software
Version
5.2.21(1)
3.11
1.21.4
4.9
3.2.1
1.0.0
2.5.8
1.13
2.3.0
1.4-r122
Q: What’s the version of R packages used in your studies?
A: See the following code snippet:
library(biomaRt) library(tidyverse) library(Seurat) library(scDesign2) library(arrow) sessionInfo()
R version 4.3.2 (2023-10-31) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Kali GNU/Linux Rolling Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/openblas-openmp/libblas.so.3 LAPACK: /usr/lib/x86_64-linux-gnu/openblas-openmp/libopenblasp-r0.3.26.so; LAPACK version 3.12.0 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=en_US.UTF-8 [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 time zone: Asia/Shanghai tzcode source: system (glibc) attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] arrow_15.0.1 scDesign2_0.1.0 Seurat_5.0.3 SeuratObject_5.0.1 sp_2.1-3 [6] lubridate_1.9.3 forcats_1.0.0 stringr_1.5.1 dplyr_1.1.4 purrr_1.0.2 [11] readr_2.1.5 tidyr_1.3.1 tibble_3.2.1 ggplot2_3.5.0 tidyverse_2.0.0 [16] biomaRt_2.58.2 loaded via a namespace (and not attached): [1] RColorBrewer_1.1-3 jsonlite_1.8.8 magrittr_2.0.3 spatstat.utils_3.0-4 [5] zlibbioc_1.48.2 vctrs_0.6.5 ROCR_1.0-11 spatstat.explore_3.2-7 [9] memoise_2.0.1 RCurl_1.98-1.14 htmltools_0.5.8.1 progress_1.2.3 [13] curl_5.2.1 sctransform_0.4.1 parallelly_1.37.1 KernSmooth_2.23-22 [17] htmlwidgets_1.6.4 ica_1.0-3 plyr_1.8.9 plotly_4.10.4 [21] zoo_1.8-12 cachem_1.0.8 igraph_2.0.3 mime_0.12 [25] lifecycle_1.0.4 pkgconfig_2.0.3 Matrix_1.6-5 R6_2.5.1 [29] fastmap_1.1.1 GenomeInfoDbData_1.2.11 fitdistrplus_1.1-11 future_1.33.2 [33] shiny_1.8.1.1 digest_0.6.35 colorspace_2.1-0 patchwork_1.2.0 [37] AnnotationDbi_1.64.1 S4Vectors_0.40.2 tensor_1.5 RSpectra_0.16-1 [41] irlba_2.3.5.1 RSQLite_2.3.6 filelock_1.0.3 progressr_0.14.0 [45] spatstat.sparse_3.0-3 fansi_1.0.6 timechange_0.3.0 polyclip_1.10-6 [49] abind_1.4-5 httr_1.4.7 compiler_4.3.2 bit64_4.0.5 [53] withr_3.0.0 DBI_1.2.2 fastDummies_1.7.3 MASS_7.3-60.0.1 [57] rappdirs_0.3.3 tools_4.3.2 lmtest_0.9-40 httpuv_1.6.15 [61] future.apply_1.11.2 goftest_1.2-3 glue_1.7.0 nlme_3.1-164 [65] promises_1.3.0 grid_4.3.2 Rtsne_0.17 cluster_2.1.6 [69] reshape2_1.4.4 generics_0.1.3 spatstat.data_3.0-4 gtable_0.3.4 [73] tzdb_0.4.0 data.table_1.15.4 hms_1.1.3 xml2_1.3.6 [77] utf8_1.2.4 XVector_0.42.0 spatstat.geom_3.2-9 BiocGenerics_0.48.1 [81] RcppAnnoy_0.0.22 ggrepel_0.9.5 RANN_2.6.1 pillar_1.9.0 [85] spam_2.10-0 RcppHNSW_0.6.0 later_1.3.2 splines_4.3.2 [89] BiocFileCache_2.10.2 lattice_0.22-6 deldir_2.0-4 survival_3.5-8 [93] bit_4.0.5 tidyselect_1.2.1 Biostrings_2.70.3 miniUI_0.1.1.1 [97] pbapply_1.7-2 gridExtra_2.3 IRanges_2.36.0 scattermore_1.2 [101] stats4_4.3.2 Biobase_2.62.0 matrixStats_1.2.0 stringi_1.8.3 [105] lazyeval_0.2.2 codetools_0.2-19 cli_3.6.2 uwot_0.1.16 [109] xtable_1.8-4 reticulate_1.35.0 munsell_0.5.1 pscl_1.5.9 [113] Rcpp_1.0.12 GenomeInfoDb_1.38.8 spatstat.random_3.2-3 globals_0.16.3 [117] dbplyr_2.5.0 png_0.1-8 XML_3.99-0.16.1 parallel_4.3.2 [121] assertthat_0.2.1 blob_1.2.4 prettyunits_1.2.0 dotCall64_1.1-1 [125] bitops_1.0-7 listenv_0.9.1 viridisLite_0.4.2 scales_1.3.0 [129] ggridges_0.5.6 leiden_0.4.3.1 crayon_1.5.2 rlang_1.1.3 [133] cowplot_1.1.3 KEGGREST_1.42.0
Please note that we used OpenBLAS instead of Intel oneAPI MKL BLAS since several errors arose while using the latter.