Difference between revisions of "Darmor Tapidor"
Philippbayer (talk | contribs) (→Results) |
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[http://appliedbioinformatics.com.au/download/DarmorTapidor/GO_Arabidopsis_Terms.zip GO_Arabidopsis_Terms.zip] Swiss-Prot/''Arabidopsis'' based GO terms for Darmor and Tapidor annotation | [http://appliedbioinformatics.com.au/download/DarmorTapidor/GO_Arabidopsis_Terms.zip GO_Arabidopsis_Terms.zip] Swiss-Prot/''Arabidopsis'' based GO terms for Darmor and Tapidor annotation | ||
| − | === Tapidor === | + | === Tapidor v6.3 === |
[http://appliedbioinformatics.com.au/download/DarmorTapidor/Tapidor_v63_assembly.fasta.gz Tapidor_v63_assembly.fasta.gz] - assembly as pseudo-molecules | [http://appliedbioinformatics.com.au/download/DarmorTapidor/Tapidor_v63_assembly.fasta.gz Tapidor_v63_assembly.fasta.gz] - assembly as pseudo-molecules | ||
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[http://appliedbioinformatics.com.au/download/DarmorTapidor/Tapidor_v63_assembly.all.maker.augustus_masked.proteins_Pfam_results.gff.gz Tapidor_v63_assembly.all.maker.augustus_masked.proteins_Pfam_results.gff.gz] - PFam results for filtered predicted proteins | [http://appliedbioinformatics.com.au/download/DarmorTapidor/Tapidor_v63_assembly.all.maker.augustus_masked.proteins_Pfam_results.gff.gz Tapidor_v63_assembly.all.maker.augustus_masked.proteins_Pfam_results.gff.gz] - PFam results for filtered predicted proteins | ||
| − | === Darmor === | + | === Darmor v8.1 === |
[http://appliedbioinformatics.com.au/download/DarmorTapidor/Darmor_v81_assembly.fasta.gz Darmor_v81_assembly_fasta.gz] - assembly as pseudo-molecules | [http://appliedbioinformatics.com.au/download/DarmorTapidor/Darmor_v81_assembly.fasta.gz Darmor_v81_assembly_fasta.gz] - assembly as pseudo-molecules | ||
Revision as of 12:38, 30 September 2016
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 alignment with reference LASTZSorter.py
contigPlacer - places contigs based on recombination patterns contigPlacer
R-scripts used for plotting - Venn-diagrams, boxplots R_plotting_scripts.zip
The SkimGBS pipeline is available here: http://appliedbioinformatics.com.au/index.php/SkimGBS
Results
Tapidor genetic map from MSTMap (txt) - MSTMap_Input.zip Input file for MSTMap
Darmor SNPs anchored on Darmor v8.1 reference (gff3)
Tapidor SNPs anchored on Tapidor v6.3 reference (gff3)
Repetitive_Collapsed_Genes.zip List of genes in repetitive and collapsed regions
Repetitive_Collapsed_Regions.zip Coordinates of repetitive and collapsed regions in Darmor and Tapidor (bed)
SwissProt_Pfam_hits_Repetitive_Collapsed_Genes.zip Pfam and Swissprot results for repetitive and collapsed genes
Annotation
List of Transposase related PFAM IDs used for filtering
GO_Arabidopsis_Terms.zip Swiss-Prot/Arabidopsis based GO terms for Darmor and Tapidor annotation
Tapidor v6.3
Tapidor_v63_assembly.fasta.gz - assembly as pseudo-molecules
Tapidor_v6.3_contig_order.zip - contig positions in assembly as gff3
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 v8.1
Darmor_v81_assembly_fasta.gz - assembly as pseudo-molecules
Darmor_v8.1_contig_order.zip - order of contigs as gff3 files
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
