9 files

Hormaphis cornu gall color association studies scripts

journal contribution
posted on 14.01.2021, 21:53 by Aishwarya Korgaonkar, Clair Han, David Stern
Code used in the Hormaphis cornu genome-wide and target enrichment association study of gall color, associated with the publication "A novel family of secreted insect proteins linked to plant gall development" by Korgaonkar et al. (2021).

The scripts included here are for 4 analysis:

1) H. cornu whole genome association study
Hcor_GWAS_directAssociation.sh, samples_phenotypes.txt

2) H. cornu enrichment region around dgc association study
Hcor_enrichment_assocation_plink.sh, phenotypes_Hcor.txt

Plots for both analysis above are generated in GWAS_plots.Rmd, which include figures 2A-D.

3) PCA for both association studies above
Hcor_GWAS_PCA.sh, Hcor_GWAS_PCA.R, phenotypes.txt
Generate figures S1C-F.

4) Discordant reads mapped in enrichment region
discordant_reads.sh, resequencing_unmappedReads_TE_July2020.R
Generate figures S1G-K.

Please contact Clair Han at hanc@janelia.hhmi.org with questions.