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