GenespaceRumexComparative

genespace scripts for many Rumexes

deprecated

gsRun2024_02_07: lifted over tx haplotypes, nc haps, paucifolius haps, buceph and sagittatus gsRun2024_02_26: merged/lifted over NC and TX reference genomes, pauc, rsag, rsalicifolius, rbbuc gsRun2024_03_01: same as above, but with spp names appended to lifted over gene names to prevent confusion gsRun2024_03_25: maker annotation tx_mat and tx_pat, and Rsal. pauc, buc, nc haps and sagittatus incl. gsRun2024_06_24: buc, sag, tx_mat and tx_pat only - for dn/ds analyses. buc maker annotation, sag liftover gsRun2024_07_19: tx merged and sag only for 1-1 orthologues for differential expression stuff

buceph maker vs. gffread peptide fastas

BUSCO_buc_maker/ BUSCO_buc_gffread/ agat/

contig maps with telomeres labeled

contigmap_telo_buc.pdf contigmap_telo_pauc_hap1.pdf contigmap_telo_pauc_merged.pdf contigmaps.R

genomes for genespace runs

old TX annotation, old rhast NC and TX liftover annotatinos

genomeRepo/deprecated

old lifted over TX anno with nchap gene names

genomeRepo/OldRhast_TX/

old lifted over Rsag annotation

genomeRepo/OldRsag/

lifted over buc annotatios, scaffolds 1 to 8

genomeRepo/Rbuc/

combined paucifolius hap1 and 2, lifted over

genomeRepo/Rpauc

Rsagittatus hap1, annotated separately w maker

genomeRepo/Rsag/

Rsalicifolius renamed scaffolds, annotated w maker

genomeRepo/Rsal

R hastatulus XYY NC cytotype, maternal haplotype plus Ys (not sure if includes both PARs, double check)

genomeRepo/Rhast_NC

R hast XY TX cytotype, paternal haplotype plus X (no mat PAR)

genomeRepo/Rhast_TX

haplotype-specific repos

maker annotation for r buceph

hapGenomeRepo/bucephalophorus/

various old versions of things

hapGenomeRepo/lessold_sagittatus/ hapGenomeRepo/old_sagittatus/ hapGenomeRepo/old_bucephalophorus/

paucifolius lifted over annos

hapGenomeRepo/paucifolius_hap1/ hapGenomeRepo/paucifolius_hap2/

lifted over tx annotations

hapGenomeRepo/tx_mat_lift/ hapGenomeRepo/tx_pat_lift/

rumex sagittatus maker

hapGenomeRepo/sagittatus/

Rumex salicifolius maker

hapGenomeRepo/Rsal/

XY cytotype TX haplotypes maker

hapGenomeRepo/tx_mat hapGenomeRepo/tx_pat

XYY cytotype NC haplotypes maker

hapGenomeRepo/nc_hap1 hapGenomeRepo/nc_hap2