Supplementary files and code for the "The genomic origin of the unique chaetognath body plan" ATAC-seq Processing of called peaks (bed) descripting classif-atac.ipynb and resulting called peaks in peaks_all_re.txt and filtered version peaks_flt_re.txt. GeneFamilies Code used for gene family analyses is detailed in gene_families 2.ipynb using as input: - the gene families inferred by Broccoli orthologous_groups_eq.txt - the reconciliated gene trees calculated by GeneRax as NHS format: Chaeto_rev0124_recon.nhx and also as XML in xml/Chaeto_rev0124_recon_xml.tgz with the corresponding code to parse them. The file Chaeto_rev0124_recon.lab.tre has the same trees in a human readable foramt with the gene names for mouse and Drosophila. Resulting files include - the list of gained, lost and duplicated gene families:Orthogroups_GLD_re - GO enrichment for chaetognath duplicates: Pgot_DupGO_enrch_r_BP_wn.tsv - script used to compute 4DTv stats4D.py from reciprocal gene alignements PargotALI.out.gz. Results are in PargotALI.stats.gz - Panther_all.txt contains panther annotation for all the proteomes. - emapper/*.emapper.annotations.gzcontains the eggnog annotation for selected proteomes - GenEra_34758_gene_ages.tsv is the result of GenEra phylostratigraphic analyses - loss_gnathi_bflo.txt: amphioxus homologues of genes lost in the gnathiferan lineages - proteomes-pgot-sel.tgz: proteomes of selected genes used for gene family reconstruction Methylation - Script_Chaeto.R: R script to perform data analysis and plotting - ChaetoDeepToolsCommands.sh: plots of methylation in genes and TEs - EMseq_files.tar.gz: result file from EM-seq - Methylated_genes.tsv: list of methylated genes - MethylationToolkitGenes.txt: analyseis of methylation toolkit - Paraspadella_EMseq.CGmap.gz: EMSeq genome-wide map OperonTransSplicing - SL_Operon_redux-chim.ipynb: notebook describing the annotation of operons - SL_status_eq.txt: SL assigned to genes - go-basic.obo: gene ontology file - Pgot_lowinput_SLs_counts_eq.tsv: counts of splice-leaders detetected for transcripts of annotated genes - Pgot_operons_filt_eq.txt: list of annotated operons - Pgot_OvL0Qm.cro.sizes: list of chromsome and scaffold sizes - Pgot_oper_GOe_eq.tsv: GO enrichment in operons Ressources Main ressource files including : - Pgot_OvL0Qm_cn.fa.gz: genome fasta file - Pgot_OvL0Qm_aPe.gtf.gz: GTF file - Pgot_genInfo_rr.txt: list of genes with function annotation, gene family, domains, phylostrata, etc... - Pgot_OvL0Qm_aP.repeats.cro.bed: BED files with positions of repeats Single-cell - SAMap_vignette.ipynb: notebook describing how to run SAMap. - markers.tsv: list of cell-types marker genes inferred using Seurat - ChaetoGN_Lau.Rmd: R markdown summarising main analyses steps - Ch_v5_chim.RDS: R object containing the analyses datasets - maps/*: results of SAMAP comparisons Hi-C - NOTEBOOK_all_hic_analyses.ipynb detailed the analyses of Hi-C data using other scripts and files in this folder - data` contains main Hi-C datafiles including multires contact map chaeto.matrix.final.allres.hic