Difference between revisions of "Darmor Tapidor"
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Collinearity analysis - parses MCScanX results and checks for missing genes in expected regions [http://appliedbioinformatics.com.au/download/DarmorTapidor/Collinearity_scripts.zip Collinearity_scripts.zip] | Collinearity analysis - parses MCScanX results and checks for missing genes in expected regions [http://appliedbioinformatics.com.au/download/DarmorTapidor/Collinearity_scripts.zip Collinearity_scripts.zip] | ||
| − | LASTZSorter.py - sorts contigs based on LASTZ | + | LASTZSorter.py - sorts contigs based on LASTZ alignment with reference [http://appliedbioinformatics.com.au/download/DarmorTapidor/LASTZSorter.py LASTZSorter.py] |
contigPlacer - places contigs based on recombination patterns [https://github.com/philippbayer/contigplacer contigPlacer] | contigPlacer - places contigs based on recombination patterns [https://github.com/philippbayer/contigplacer contigPlacer] | ||
Revision as of 07:48, 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)
Darmor SNPs anchored on Darmor v8.1 reference (gff3)
Tapidor SNPs anchored on Tapidor v6.3 reference (gff3)
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
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
Darmor_v81_assembly_fasta.gz - assembly as pseudomolecules
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
