Last updated: 2024-01-29
Checks: 7 0
Knit directory:
locust-comparative-genomics/
This reproducible R Markdown analysis was created with workflowr (version 1.7.1). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.
Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.
Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.
The command set.seed(20221025) was run prior to running
the code in the R Markdown file. Setting a seed ensures that any results
that rely on randomness, e.g. subsampling or permutations, are
reproducible.
Great job! Recording the operating system, R version, and package versions is critical for reproducibility.
Nice! There were no cached chunks for this analysis, so you can be confident that you successfully produced the results during this run.
Great job! Using relative paths to the files within your workflowr project makes it easier to run your code on other machines.
Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.
The results in this page were generated with repository version 4246194. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.
Note that you need to be careful to ensure that all relevant files for
the analysis have been committed to Git prior to generating the results
(you can use wflow_publish or
wflow_git_commit). workflowr only checks the R Markdown
file, but you know if there are other scripts or data files that it
depends on. Below is the status of the Git repository when the results
were generated:
Ignored files:
Ignored: .DS_Store
Ignored: .RData
Ignored: .Rhistory
Ignored: .Rproj.user/
Ignored: analysis/.DS_Store
Ignored: analysis/.Rhistory
Ignored: data/.DS_Store
Ignored: data/.Rhistory
Ignored: data/metadata/.DS_Store
Ignored: figures/
Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.
These are the previous versions of the repository in which changes were
made to the R Markdown
(analysis/2_orthologs-prediction.Rmd) and HTML
(docs/2_orthologs-prediction.html) files. If you’ve
configured a remote Git repository (see ?wflow_git_remote),
click on the hyperlinks in the table below to view the files as they
were in that past version.
| File | Version | Author | Date | Message |
|---|---|---|---|---|
| html | f701a01 | Maeva A. TECHER | 2024-01-29 | reupdate |
| html | 2ca8696 | Maeva A. TECHER | 2024-01-29 | Build site. |
| html | 5c5487e | Maeva A. TECHER | 2024-01-29 | Build site. |
| html | 0135a6e | Maeva A. TECHER | 2024-01-29 | Build site. |
| Rmd | 505a8dc | Maeva A. TECHER | 2024-01-29 | wflow_publish("analysis/2_orthologs-prediction.Rmd") |
| html | 579056a | Maeva A. TECHER | 2024-01-29 | Build site. |
| Rmd | f50a3dd | Maeva A. TECHER | 2024-01-29 | wflow_publish("analysis/2_orthologs-prediction.Rmd") |
| html | f831779 | Maeva A. TECHER | 2024-01-24 | Build site. |
| html | 1b09cbe | Maeva A. TECHER | 2024-01-24 | remove |
| html | 79006db | Maeva A. TECHER | 2024-01-24 | Build site. |
| Rmd | b195f57 | Maeva A. TECHER | 2024-01-23 | refresh |
| html | b195f57 | Maeva A. TECHER | 2024-01-23 | refresh |
| html | dfc68c7 | Maeva A. TECHER | 2023-12-18 | Build site. |
| Rmd | 53877fa | Maeva A. TECHER | 2023-12-18 | add pages |
We wanted to compare the six genomes of Schistocerca to get insights on gene evolution and relationships regarding their numbers, content, function and location. In order to achieve this, we need to identify groups of orthologous genes among our species of interest, considering at least one outgroup.
Orthologs are genes from different species that originated from a single ancestral gene and evolved through speciation events. However since genes can be lost or duplicated during evolution, some genes may not have exactly one orthologue in the genome of another species. Here we will separate the 1:1 orthologs to the the concept of orthogroups. Orthogroups can contain 1:1 orthologs but also several several orthologs from different species, including paralogs and one-to-many orthologs. Paralogs are genes within the same species that have originated from a shared ancestral genes but have diverged over time following gene duplication events.
IMPORTANT. We used OrthoFinder to identify the orthogroups using amino acid sequences from the longest isoform of each gene. For this part, refers to the pipeline FormicidaeMolecularEvolution by Megan Barkdull. We describe below the modifications made.
Using the create file “input-XXX.txt” we downloaded the coding sequence, protein sequence, GFF annotation data for each of our six Schistocerca species and one termites outgroup Csec.
./scripts/DataDownload ./scripts/input-XXX.txt…WRITING/FORMATTING ONGOING
If you use this script, please cite:
Emms D.M. & Kelly S. (2019), Genome Biology 20:238
If you use the species tree in your work then please also cite:
Emms D.M. & Kelly S. (2017), MBE 34(12): 3267-3278 Emms D.M. & Kelly S. (2018), bioRxiv https://doi.org/10.1101/267914
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
other attached packages:
[1] workflowr_1.7.1
loaded via a namespace (and not attached):
[1] vctrs_0.6.5 httr_1.4.7 cli_3.6.2 knitr_1.45
[5] rlang_1.1.3 xfun_0.41 stringi_1.8.3 processx_3.8.3
[9] promises_1.2.1 jsonlite_1.8.8 glue_1.7.0 rprojroot_2.0.4
[13] git2r_0.33.0 htmltools_0.5.7 httpuv_1.6.13 ps_1.7.5
[17] sass_0.4.8 fansi_1.0.6 rmarkdown_2.25 jquerylib_0.1.4
[21] tibble_3.2.1 evaluate_0.23 fastmap_1.1.1 yaml_2.3.8
[25] lifecycle_1.0.4 whisker_0.4.1 stringr_1.5.1 compiler_4.3.1
[29] fs_1.6.3 pkgconfig_2.0.3 Rcpp_1.0.12 rstudioapi_0.15.0
[33] later_1.3.2 digest_0.6.34 R6_2.5.1 utf8_1.2.4
[37] pillar_1.9.0 callr_3.7.3 magrittr_2.0.3 bslib_0.6.1
[41] tools_4.3.1 cachem_1.0.8 getPass_0.2-4