Last updated: 2024-02-14

Checks: 6 1

Knit directory: locust-comparative-genomics/

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Repository version: e39d280

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File Version Author Date Message
html e39d280 Maeva A. TECHER 2024-01-29 Build site.
html f701a01 Maeva A. TECHER 2024-01-29 reupdate
html be046c6 Maeva A. TECHER 2024-01-24 Build site.
html 1b09cbe Maeva A. TECHER 2024-01-24 remove
html 141b63c Maeva A. TECHER 2023-12-18 Build site.
Rmd 53877fa Maeva A. TECHER 2023-12-18 add pages

At this point, we will have organized both SRA and de novo paired-end sequencing data within our reads directory located at /scratch/group/songlab/maeva/headthor-locusts-rna/{species}/data/reads and will be ready to run the Snakemake pipeline on it. As a reminder, each library corresponds to the transcriptome of bulk tissues (either head or thorax) from a single specimen reared under isolated or crowded conditions.

Control the quality of the .fastq files

The first step is to ensure that we have enough reads per library and remove any potential outlier resulting from library preparation or sequencing failure. For that, we will assess each .fastq file with FASTQC. However, considering we are working with a significant sample size, we will compile the results using MULTIQC.

The aggregated results can be conveniently viewed by opening the HTML report in a web browser.


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: America/Chicago
tzcode source: internal

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

loaded via a namespace (and not attached):
 [1] vctrs_0.6.5       cli_3.6.2         knitr_1.45        rlang_1.1.3      
 [5] xfun_0.41         stringi_1.8.3     promises_1.2.1    jsonlite_1.8.8   
 [9] workflowr_1.7.1   glue_1.7.0        rprojroot_2.0.4   git2r_0.33.0     
[13] htmltools_0.5.7   httpuv_1.6.14     sass_0.4.8        fansi_1.0.6      
[17] rmarkdown_2.25    jquerylib_0.1.4   evaluate_0.23     tibble_3.2.1     
[21] fastmap_1.1.1     yaml_2.3.8        lifecycle_1.0.4   whisker_0.4.1    
[25] stringr_1.5.1     compiler_4.3.1    fs_1.6.3          Rcpp_1.0.12      
[29] pkgconfig_2.0.3   rstudioapi_0.15.0 later_1.3.2       digest_0.6.34    
[33] R6_2.5.1          utf8_1.2.4        pillar_1.9.0      magrittr_2.0.3   
[37] bslib_0.6.1       tools_4.3.1       cachem_1.0.8