Darmor Tapidor

This page collects the files for Bayer et al. B. napus Darmor/Tapidor genome paper

Software

Collinearity analysis - parses MCScanX results and checks for missing genes in expected regions Collinearity_scripts.zip

LASTZSorter.py - sorts contigs based on LASTZ output LASTZSorter.py

contigPlacer - places contigs based on recombination patterns contigPlacer

R-scripts used for plotting - Venn-diagrams, boxplots R_plotting_scripts.zip

Results

Genetic map from MSTMap

Darmor SNPs anchored on Darmor v8.1 reference

Tapidor SNPs anchored on Tapidor v6.3 reference

Annotation

List of Transposase related PFAM IDs used for filtering

Tapidor

Tapidor_v63_assembly.fasta.gz - assembly as pseudo-molecules

Filtered annotation

No AED=1 scores, transcripts longer than 100 bp, no Transposase domains

Tapidor_v63_assembly.augustus_masked_filtered.gff.gz - filtered predicted annotation in GFF format

Tapidor_v63_assembly.all.maker.augustus_masked.transcripts_filtered.fasta.gz - filtered predicted transcripts

Tapidor_v63_assembly.all.maker.augustus_masked.proteins_filtered.fasta.gz - filtered predicted proteins

Tapidor_v63_assembly.all.maker.augustus_masked.proteins_Pfam_results.gff.gz - PFam results for filtered predicted proteins

Darmor

Darmlr_v81_assembly_fasta.gz - assembly as pseudomolecules

Filtered annotation

No AED=1 scores, transcripts longer than 100 bp, no Transposase domains

Darmor_v81_assembly.augustus_masked_filtered.gff.gz - filtered predicted annotation in GFF format

Darmor_v81_assembly.all.maker.augustus_masked.transcripts_filtered.fasta.gz - filtered predicted transcripts

Darmor_v81_assembly.all.maker.augustus_masked.proteins_filtered.fasta.gz - filtered predicted proteins

Darmor_v81_assembly.all.maker.augustus_masked.proteins_Pfam_results.gff.gz - PFam results for filtered predicted proteins