Difference between revisions of "Darmor Tapidor"
Philippbayer (talk | contribs) (→Results data files) |
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== Software == | == Software == | ||
− | Collinearity analysis - [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 [http://appliedbioinformatics.com.au/download/DarmorTapidor/LASTZSorter.py LASTZSorter.py] | + | LASTZSorter.py - sorts contigs based on LASTZ output [http://appliedbioinformatics.com.au/download/DarmorTapidor/LASTZSorter.py LASTZSorter.py] |
− | contigPlacer [https://github.com/philippbayer/contigplacer contigPlacer] | + | contigPlacer - places contigs based on recombination patterns [https://github.com/philippbayer/contigplacer contigPlacer] |
+ | |||
+ | R-scripts used for plotting - Venn-diagrams, boxplots [http://appliedbioinformatics.com.au/download/DarmorTapidor/R_plotting_scripts.zip R_plotting_scripts.zip] | ||
== Results == | == Results == |
Revision as of 07:20, 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 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