The genomic origin of the unique chaetognath body plan

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