Scripts used to process and analyze the RNA-seq data from Drosophila melanogaster ovariole morphogenesis and reproduce the results from the article "Distinct gene expression dynamics in germ line and somatic tissue during ovariole morphogenesis in Drosophila melanogaster"
"Distinct gene expression dynamics in germ line and somatic tissue during ovariole morphogenesis in Drosophila melanogaster"
Shreeharsha Tarikere, Guillem Ylla, and Cassandra G. Extavour
Department of Organismic and Evolutionary Biology, Harvard University
April 2021
Repository content:
- Run_RSEM_batch.sh: Sbatch script to map RNA-seq reads in the cluster using STAR (2.7.6a) within RSEM (1.3.3) on the Drosophila melanogaster genome (Dmel6.36).
- 1-Whole_Ovary_libraries: Scripts for analyzing whole ovary RNA-seq dataset.
- 1-Whole_Ovary_libraries.Rmd: Rmd file with the R code
- 1-Whole_Ovary_libraries.html: Compiled R script in html.
- 2-Tissue_Specific_Ovary_libraries: Scripts for analyzing the libraries of ovary germ and somatic tissues. Includes Differential Expression Analysis, KENN & GO enrichment analysis, and multiple plots.
- 2-Tissue_Specific_Ovary_libraries.Rmd: Rmd file with the R code
- 2-Tissue_Specific_Ovary_libraries.html: Compiled R script in html.
- data directory: Contains large data files such as tables of counts and metadata files. Raw data and tables of counts also available at GSE172015.
- Aux_functions.R: Functions used along the project, mainly to determine and keep consistent with the colors
- Session_info.txt: Information about the package versions used in the analysis.