Last updated: 2023-11-24
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | a55e367 | Dave Tang | 2023-11-24 | Getting started with Cell Ranger |
Cell Ranger is a set of analysis pipelines that process Chromium single cell 3’ and 5’ scRNA-seq data. The pipelines process raw sequencing output, performs read alignment, generate gene-cell matrices, and can perform downstream analyses such as clustering and gene expression analysis. Cell Ranger includes the following pipelines:
You can download Cell Ranger from their software download page. Conveniently, Cell Ranger is provided as a single self-contained file that bundles all its own software dependencies. You can view the source at their GitHub repository, which does not look like it is being actively maintained anymore.
First, start downloading some input data that we will use later in the post; they are quite large and depending on your Internet speed, may take a long time.
wget -c https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-exp/6.1.0/40k_NSCLC_DTC_3p_HT_nextgem_Multiplex/40k_NSCLC_DTC_3p_HT_nextgem_Multiplex_fastqs.tar
wget -c https://cf.10xgenomics.com/samples/cell-exp/6.1.0/40k_NSCLC_DTC_3p_HT_nextgem_Multiplex/40k_NSCLC_DTC_3p_HT_nextgem_Multiplex_config.csv
wget -c https://cf.10xgenomics.com/samples/cell-exp/6.1.0/40k_NSCLC_DTC_3p_HT_nextgem_Multiplex/40k_NSCLC_DTC_3p_HT_nextgem_Multiplex_count_feature_reference.csvNext, visit the download page to generate your own download link for the Cell Ranger tarball.
wget -O cellranger-6.1.2.tar.gz "https://cf.10xgenomics.com/releases/cell-exp/cellranger-6.1.2.tar.gz?Expires=1648564870&Policy=eyJTdGF0ZW1lbnQiOlt7IlJlc291cmNlIjoiaHR0cHM6Ly9jZi4xMHhnZW5vbWljcy5jb20vcmVsZWFzZXMvY2VsbC1leHAvY2VsbHJhbmdlci02LjEuMi50YXIuZ3oiLCJDb25kaXRpb24iOnsiRGF0ZUxlc3NUaGFuIjp7IkFXUzpFcG9jaFRpbWUiOjE2NDg1NjQ4NzB9fX1dfQ__&Signature=LeJDJcPn5URO~zx20buwkpJ6TD9rf5UkQCFpUP5Ji~d--kauzGCDj1arQqkuM16M1QAFudP-iNb4fr1pE6nqKr12Onj7mFzZwxWvfDsqK8IuUYj0YN6jQ1nBHeu~D6-UjNHDkLTVtrC-dqxq-faUfjNUbkPJwFUSgiP1VBMiTFnGXxM8EcIOMDCvCXrhzjrbRle94O4OcUAK~Go40oyQLbHLyHOB29IhhUE1C5fRSFQ9rMB88fbxzl5IPmKAg~7TM1jH3rbz9u9HuEgdV1tL1mR9vmSfIzKep~6M-cyGKkVAdPoCdgeuZf8UihRdIhnNZH3ukIy969AorVtLYjWXWg__&Key-Pair-Id=APKAI7S6A5RYOXBWRPDA"Download the hg38 reference tarball.
wget https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-GRCh38-2020-A.tar.gzThe official Cell Ranger install page for more information has more detailed information for setting up Cell Ranger.
tar xzf cellranger-6.1.2.tar.gz
tar xzf refdata-gex-GRCh38-2020-A.tar.gz
sessionInfo()R version 4.3.2 (2023-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.3 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so; LAPACK version 3.10.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
time zone: Etc/UTC
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] workflowr_1.7.1
loaded via a namespace (and not attached):
[1] vctrs_0.6.4 httr_1.4.7 cli_3.6.1 knitr_1.45
[5] rlang_1.1.2 xfun_0.41 stringi_1.7.12 processx_3.8.2
[9] promises_1.2.1 jsonlite_1.8.7 glue_1.6.2 rprojroot_2.0.4
[13] git2r_0.32.0 htmltools_0.5.7 httpuv_1.6.12 ps_1.7.5
[17] sass_0.4.7 fansi_1.0.5 rmarkdown_2.25 jquerylib_0.1.4
[21] tibble_3.2.1 evaluate_0.23 fastmap_1.1.1 yaml_2.3.7
[25] lifecycle_1.0.3 whisker_0.4.1 stringr_1.5.0 compiler_4.3.2
[29] fs_1.6.3 pkgconfig_2.0.3 Rcpp_1.0.11 rstudioapi_0.15.0
[33] later_1.3.1 digest_0.6.33 R6_2.5.1 utf8_1.2.4
[37] pillar_1.9.0 callr_3.7.3 magrittr_2.0.3 bslib_0.5.1
[41] tools_4.3.2 cachem_1.0.8 getPass_0.2-2