G4-stemloop

The repository contains all the code required to run the stem loop test of G-quadruplex and generate results.

1 map G4 across seven primate species' T2T genomes

2 identify ape shared G4s and build substitution spectrum

To identify substitutions in chimp:

for i in {1..22} ; do Rscript chimpid_snp_count_sharedG4_noanc.R $i; done
Rscript chimpid_snp_count_sharedG4_noanc.R "X"
Rscript chimpid_snp_count_sharedG4_noanc.R "Y"
Rscript shared_substitution_chimp_hsachr.R
sbatch intersect_infer_chimp_hsachr.sh \

sbatch intersect_g4_stemloop_subsets.sh "/human_lost/chimp_id"
sbatch intersect_g4_stemloop_subsets.sh "/chimp_specific/chimp_id"
sbatch intersect_g4_stemloop_subsets.sh "/chimp_specific/chimp_id"
sbatch intersect_g4_stemloop_subsets.sh "/shared_g4/chimp_id"
sbatch intersect_g4_stemloop_subsets.sh "/disappear_g4_in_orang/chimp_id"
sbatch intersect_g4_stemloop_subsets_human.sh "/disappear_g4_in_orang"
sbatch intersect_g4_stemloop_subsets_human.sh "/shared_g4"
sbatch intersect_g4_stemloop_subsets_human.sh "/unique_g4"
sbatch intersect_g4_stemloop_subsets_human.sh "/disappear_g4" \

Rscript compare_sequence_divergence.R

3 HKA test and visualization

Rscript HKA_test_fig3_4.R

4 PhyloFit test