Installation

Install zUMIs

zUMIs is a command line tool written in perl, shell and R. zUMIs can be installed by installing the dependencies and cloning the repository as given below.

git clone https://github.com/sdparekh/zUMIs.git

Alternatively, you can start your own Amazon cloud instance with zUMIsor use a Docker containing zUMIs!

Dependencies

General

• samtools >= 1.5 🔧 [tested: 1.7, 1.9] Note: For non-UMI based methods, it is highly recommended to use samtools 1.7 and higher.
• STAR >= 2.5.4b 🌟 [RECOMMENDED: 2.5.4b or 2.7.X] Note: Some users have reported that some STAR versions (e.g. 2.6.0a) may produce problems when generating the reference index without GTF files.
• R >= 3.4 💻 [tested: 3.4.4, 3.5.2, 3.6.0]
• pigz >= 2.3 🐷 [tested: 2.4]

R

To install R dependencies, please run the following:

cran_pcks <- c("inflection","yaml","shiny","shinythemes","shinyBS","ggplot2","mclust","dplyr","cowplot","Matrix","BiocManager","devtools","stringdist","data.table","stringr","extraDistr")
install.packages(cran_pcks)
bioc_pcks <- c("GenomicRanges","GenomicFeatures","GenomicAlignments","AnnotationDbi","GenomeInfoDb","plyranges")
BiocManager::install(bioc_pcks)
devtools::install_github('VPetukhov/ggrastr')

Optional

For faster demultiplexing of per-cell bam files, please have a valid installation of python3.x and the pysam (>=0.15) module.

R packages

For bioconductor version numbers, please check the sessionInfo() output of a validated zUMIs installation below:

> sessionInfo()
R version 3.4.4 (2018-03-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 9 (stretch)

Matrix products: default
BLAS: /usr/lib/atlas-base/atlas/libblas.so.3.0
LAPACK: /usr/lib/lapack/liblapack.so.3.7.0

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       

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets
[8] methods   base     

other attached packages:
 [1] Rsubread_1.28.1            GenomicAlignments_1.14.2  
 [3] Rsamtools_1.30.0           Biostrings_2.46.0         
 [5] XVector_0.18.0             SummarizedExperiment_1.6.3
 [7] DelayedArray_0.2.7         matrixStats_0.53.1        
 [9] GenomicFeatures_1.30.3     AnnotationDbi_1.38.2      
[11] Biobase_2.38.0             GenomicRanges_1.30.1      
[13] GenomeInfoDb_1.14.0        IRanges_2.12.0            
[15] S4Vectors_0.16.0           BiocGenerics_0.24.0       
[17] Matrix_1.2-14              cowplot_0.8.0             
[19] dplyr_0.7.2                mclust_5.3                
[21] ggplot2_2.2.1              shinyBS_0.61              
[23] shinythemes_1.1.1          shiny_1.0.5               
[25] yaml_2.1.18               

loaded via a namespace (and not attached):
 [1] lattice_0.20-35        colorspace_1.3-2       htmltools_0.3.6       
 [4] rtracklayer_1.38.3     blob_1.1.0             XML_3.98-1.9          
 [7] rlang_0.1.2            glue_1.2.0             DBI_0.7               
[10] BiocParallel_1.12.0    bit64_0.9-7            bindrcpp_0.2.2        
[13] GenomeInfoDbData_1.0.0 bindr_0.1.1            plyr_1.8.4            
[16] zlibbioc_1.24.0        munsell_0.4.3          gtable_0.2.0          
[19] memoise_1.1.0          biomaRt_2.32.1         httpuv_1.3.5          
[22] Rcpp_0.12.16           xtable_1.8-2           scales_0.5.0          
[25] mime_0.5               bit_1.1-12             RMySQL_0.10.13        
[28] digest_0.6.15          grid_3.4.4             tools_3.4.4           
[31] bitops_1.0-6           magrittr_1.5           lazyeval_0.2.1        
[34] RCurl_1.95-4.10        tibble_1.3.4           RSQLite_2.0           
[37] pkgconfig_2.0.1        assertthat_0.2.0       R6_2.2.2              
[40] compiler_3.4.4