H. cornu classifier-identified bicycle genes expression scripts

Code for generating the H. cornu bicycle genes characterizations and expression analysis from publication "Gene structure-based homology search identifies highly divergent putative effector gene family", Stern and Han, BioRxiv https://doi.org/10.1101/2021.09.24.461719.

H. cornu bicycle genes characterization:

Hcor_cluster_analysis_v5.5.6.Rmd

Inputs: Augustus.updated_w_annots.3ix21_final.pep.fa

gene_cluster2.names

Hcor_bicycle_classifier_0.72cutoff_FP_transcripts_v5.5.6.txt

Generates figures 2A-C, 3 all panels

H. cornu bicycle genes expression:

Hcor_SG_DE_analysis.5.classifier_CH_7ix21.Rmd

Hcor_classifier_RNAseq.sh

Inputs: Hcor_bicycle_classifier_0.72cutoff_v5.5.6_cluster1_gene_names.txt

Hcor_bicycle_classifier_0.72cutoff_v5.5.6_cluster1_minus_g17794.t1_gene_names.txt

Hcor_bicycle_classifier_0.72cutoff_v5.5.6_cluster2_gene_names.txt

Generates figures 2E-G, 6C

See related materials in collection at https://doi.org/10.25378/janelia.c.5778905.