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data_essential.list
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# 01_sample_info
data/maps/point_data.csv
data/r_essentials/mapping_stats.rds
# 02 qc
data/hpc/vcf_filtering/Adigi.v2.filtered.idepth
data/hpc/vcf_filtering/Adigi.v2.filtered.imiss
data/hpc/vcf_filtering/Adigi.v2.filtered.snpden
# 03 phasing
data/hpc/phasing/imputation_check.txt
data/hpc/phasing/compare_imputation_with_af.txt
# 04_popgen
data/hpc/popgen/plink2.het
data/hpc/popgen/inshore.filtered_windowed.pi
data/hpc/popgen/northoffshore.filtered_windowed.pi
data/hpc/popgen/southoffshore.filtered_windowed.pi
data/hpc/popgen/inshore.filtered_windowed.td
data/hpc/popgen/northoffshore.filtered_windowed.td
data/hpc/popgen/southoffshore.filtered_windowed.td
data/r_essentials/ld_summary_data.rds
data/hpc/private_alleles/0.9.priv
data/hpc/private_alleles/1.0.priv
# 05_popstructure
data/hpc/pca/Adigitifera_smartpca.evec
data/hpc/pca/Adigitifera_smartpca.eval
data/hpc/admixture/sample_order.txt
data/hpc/admixture/Adigitifera_ldpruned.2.Q
data/hpc/admixture/Adigitifera_ldpruned.3.Q
data/hpc/admixture/Adigitifera_ldpruned.4.Q
data/hpc/admixture/Adigitifera_ldpruned.5.Q
data/hpc/admixture/CV.txt
data/r_essentials/pcloadings.png
# 06 ibd hbd
data/hpc/ibd/Adigi_ind74.ibd_relatedness.txt
data/hpc/pcangsd/samples.txt
data/hpc/pcangsd/wa_bam.txt
data/hpc/ibdseq/1M_scaffolds.hbd
data/hpc/pcangsd/all.lengths.scaf.txt
data/hpc/ibdseq/hbd_midpoints.scaff.txt
# 07 demography
data/r_essentials/psmc.jpg
data/hpc/demography/estimate_em50_k40/em50_k40.csv
data/r_essentials/smc_bs.rds
data/nature07158-s2.txt
# 08_ehh
data/hpc/ragtag/all.lengths.scaf.txt
data/r_essentials/08_window_stats.rds
data/r_essentials/top_ehh_g3.rds
# 09_annotate_genes
data/hpc/annotation/all_ipr.tsv
data/hpc/annotation/Adigitifera_uniprot_blastp.outfmt6
data/hpc/annotation/Adigitifera_uniprot_blastx.outfmt6
data/hpc/annotation/uniprot-yourlist.xlsx
data/hpc/annotation/allgenes_ids_extracted_from_gff.txt
data/genome/adig-v2-ncbi.gff
# 10_identify windows
data/r_essentials/10_windowed_ehh.rds
data/hpc/annotation/allgenes.bed
data/r_essentials/candidate_regions_genes_ehh.rds
# 12_pbs
data/r_essentials/pbsdata.rds
data/hpc/pcangsd/all.lengths.scaf.txt
# 14_ehh_pbs
data/hpc/ragtag/ehh_sweeps_scaff.tsv
data/hpc/ragtag/all.lengths.scaf.txt
data/hpc/selection2/pbs/pbs_sweeps.scaff.tsv
data/r_essentials/pbs_thresholds.rds
# 15_GO_enrichment
# 17_dating (work in progress)
data/hpc/startmrca/regions/BLFC01000154_250000_300001_aaref.vcf
data/r_essentials/17_tmrca_data.rds
# 18 Check
data/hpc/radseq_data/out.relatedness2
data/hpc/radseq_data/Sample_list_Jia_popgen_141121.xlsx
data/hpc/radseq_data/Complete_list_Adigi_Ashmore_Adele_Beagle_Rowleys_181121.xlsx
#22a FSC Fitting
data/hpc/demography/fastsimcoal/n_parameters.txt
data/hpc/demography/fastsimcoal/divergence/split_IN_ALL.param
data/hpc/demography/fastsimcoal/divergence/split_NO_ALL.param
data/hpc/demography/fastsimcoal/divergence/split_SO_ALL.param
data/hpc/demography/fastsimcoal/divergence/split_poly_ALL.param
data/r_essentials/tested_models.png
data/hpc/demography/fastsimcoal/final2705/0.growth_rate_SI_ALL.param
data/hpc/demography/fastsimcoal/final2705/1.growth_rate_IM_ALL.param
data/hpc/demography/fastsimcoal/final2705/3.growth_rate_SC_ALL.param
data/hpc/demography/fastsimcoal/final2705/4.growth_rate_SC2_ALL.param
data/hpc/demography/fastsimcoal/final2705/6.growth_rate_AM2_ALL.param
data/hpc/demography/fastsimcoal/final2705/7.growth_rate_AM_ALL.param
data/hpc/demography/fastsimcoal/final2705/bootstrap_params.txt
#22b FSC Sim
data/hpc/demography/fastsimcoal/final2705/bootstrap_params.txt
data/r_essentials/22b_hbd_data.rds
data/r_essentials/22b_het_data.rds
data/r_essentials/22b_td_data.rds
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/admixture/3.out.growth_rate_SC_ldpruned.3.Q
data/hpc/fastsimcoal/growth_rate_SC/3.out.growth_rate_SC/admixture/3.out.growth_rate_SC_1_1.fam
data/r_essentials/22b_pbs_combined_long.rds
data/hpc/selection2/pbs/pbs_sweeps.tsv
# 23 Symbionts
data/r_essentials/23_mpa_data.rds
data/hpc/pcangsd/samples.txt
data/hpc/symbiont/ITS2_reads_mapping/sample_it2_div.txt
data/hpc/symbiont/d2s/wa_matrix.txt
# 24 Simulation without bottleneck
data/r_essentials/24_fst.rds
data/hpc/fastsimcoal/no_bott/3.out.no_bott/pca/3.out.no_bott_1_1.eigenvec
# 25 GEVA
data/hpc/vcsq/s0150.g24.csq.tsv
data/r_essentials/geva_pos.rds
data/hpc/vcsq/s0150.g24.mod.gff
# 27 Peroxidases
data/hpc/peroxidases/px_align.fasta.treefile
data/hpc/peroxidases/px_align.fasta
# x10 outgroup analysis
data/hpc/pcangsd/samples.txt
data/hpc/pcangsd/all_bam.txt
data/hpc/pcangsd/jpwa.cov
data/hpc/pcangsd/jpwa.tree
data/hpc/iqtree/partition.nex.best_scheme.nex.treefile
# x20 fineStructure
data/hpc/fineStructure/adigitifera_linked.chunkcounts.out
data/hpc/fineStructure/adigitifera_linked_mcmc.xml
data/hpc/fineStructure/adigitifera_linked_tree.xml
# x30 Ragtag
data/hpc/ragtag/ragtag_output/ragtag.scaffolds.agp
# x40 LiftOver
data/genome/oist_lengths.txt
data/genome/ncbi_lengths.txt
data/genome/oist_genes.bed
data/genome/ncbi_genes.bed
data/genome/adig-v2-ncbi.gff