Last updated: 2023-12-18

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Knit directory: locust-comparative-genomics/

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File Version Author Date Message
Rmd 53877fa Maeva A. TECHER 2023-12-18 add pages

Work environment

Environment

  • Grace Cluster at Texas A&M University, College Station, Texas, USA
  • Local Mac: macOS Monterey Version 12.6
  • R version 4.2.1

Directories

Path Purpose
/scratch/user/XXXX/locust-phase Working repository
/scratch/user/XXXX/locust-phase/workflow Location of the Snakemake pipeline
/scratch/user/XXXX/refgenomes/locust-complete Reference genome, annotation and index
/scratch/user/XXXX/locust-phase/data/reads Raw FASTQ.GZ files
/scratch/user/XXXX/locust-phase/data/kaiju Kaiju database and output
/scratch/user/XXXX/locust-phase/data/trimming Trimmed FASTQ files
/scratch/user/XXXX/locust-phase/data/alignment/STAR Output from STAR
/scratch/user/XXXX/locust-phase/data/alignment/STAR_SALMON Output from STAR-Salmon
/scratch/user/XXXX/locust-phase/data/alignment/STAR_RSEM Output from STAR-Salmon
/scratch/user/XXXX/locust-phase/data/analysis R analysis (DGE)

Snakemake pipeline

We use a Snakemake pipeline for each species. Therefore, it is essential to verify that each software is installed 1) locally or via a conda environment or 2) as a module or cloned via Github on the Grace cluster at Texas A&M University is essential.

We built our Snakemake pipeline by launching small individual jobs to tailor each cluster parameter for the best memory and time efficiency.

To ease the indexing of our file and folder, we generate some shared parameters which will be helpful in the future: 1) reference genome directory path REFdir, 2) output directory path OUTdir and 3) a list LOCUSTS containing sample base name referred as locust.

### SET DIRECTORY PATHS FOR REFERENCE AND OUTPUT DATA

REFdir = "/scratch/user/maeva-techer/refgenomes"
OUTdir = "/scratch/user/maeva-techer/locust-rna/data"

### SAMPLES LIST AND OTHER PARAMETERS

LOCUSTS, = glob_wildcards(OUTdir + "/reads/{locust}_1.fastq.gz")
print(LOCUSTS)

Softwares and database

Links to each software to add in the future

Use a conda environment

add what to install on the Macpro tower e.g., we install a conda environment called rna-seq

Use modules on Grace cluster

On Grace, each module may requires some dependencies, which is why we need to ensure they will be loaded together. For this we use the function module spider [targeted software] w/o the version.

Today we will need the following software:

  • to launch the Snakemake pipeline
module load GCC/11.2.0 OpenMPI/4.1.1 snakemake/6.10.0 Biopython/1.79
  • to perform adapter trimming and QC
module load Trimmomatic/0.39-Java-11
module load FastQC/0.11.9-Java-11
  • to perform short read mapping
module load GCC/11.2.0 STAR/2.7.9a

R packages neccessary

List of R packages used

CRAN
data.table: https://cran.r-project.org/package=data.table
dplyr: https://cran.r-project.org/package=dplyr
reshape2: https://cran.r-project.org/package=reshape2
ggplot2: https://cran.r-project.org/package=ggplot2
ggrepel: https://cran.r-project.org/package=ggrepel

Bioconductor
DESeq2: https://bioconductor.org/packages/DESeq2/
apeglm: https://bioconductor.org/packages/apeglm/
EnhancedVolcano: https://bioconductor.org/packages/EnhancedVolcano/
edgeR: https://www.bioconductor.org/packages/edgeR/


sessionInfo()
R version 4.3.1 (2023-06-16)
Platform: x86_64-apple-darwin20 (64-bit)
Running under: macOS Sonoma 14.1.2

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRblas.0.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: Asia/Tokyo
tzcode source: internal

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_1.43       
 [5] rlang_1.1.1       xfun_0.40         stringi_1.7.12    processx_3.8.2   
 [9] promises_1.2.1    jsonlite_1.8.7    glue_1.6.2        rprojroot_2.0.3  
[13] git2r_0.32.0      htmltools_0.5.6   httpuv_1.6.11     ps_1.7.5         
[17] sass_0.4.7        fansi_1.0.5       rmarkdown_2.24    jquerylib_0.1.4  
[21] tibble_3.2.1      evaluate_0.21     fastmap_1.1.1     yaml_2.3.7       
[25] lifecycle_1.0.3   whisker_0.4.1     stringr_1.5.0     compiler_4.3.1   
[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_1.2.3       
[37] pillar_1.9.0      callr_3.7.3       magrittr_2.0.3    bslib_0.5.1      
[41] tools_4.3.1       cachem_1.0.8      getPass_0.2-2