Difference between revisions of "Darmor Tapidor"
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| − | [http://appliedbioinformatics.com.au/download/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 |
Tapidor_v63_assembly.all_renamed.gff.gz - this contains all unfiltered MAKER gene models as reported by MAKER's <nowiki>gff3_merge -n -g</nowiki> | Tapidor_v63_assembly.all_renamed.gff.gz - this contains all unfiltered MAKER gene models as reported by MAKER's <nowiki>gff3_merge -n -g</nowiki> | ||
Revision as of 03:30, 26 April 2016
This page collects the files for Bayer et al. B. napus Darmor/Tapidor genome paper
Annotation
Genes and proteins were renamed from the MAKER names to the Brassica standard:
<GENUS 1 LETTER> [<species 2 letters>]<GENOME 1 LETTER>|<X>.<Chromosome number (leading zero)>g<5 digit gene model number>.g<version number>g<1 LETTER designating Genotype/line/cultivar>
So "maker-chrC04_contigs_placed_v81-snap-gene-0.93-mRNA-1 protein" becomes BnaC04g31331.2D for Darmor "new version" (of this paper), or BnaC04g31332.1T for Tapidor (first version), "maker-chrC04_contigs_placed_v81-snap-gene-0.93-mRNA-2 becomes BnaC04g31332.2D etc.
Tapidor
Tapidor_v63_assembly.fasta.gz - assembly as pseudo-molecules
Tapidor_v63_assembly.all_renamed.gff.gz - this contains all unfiltered MAKER gene models as reported by MAKER's gff3_merge -n -g
Tapidor_v63_assembly.all.maker.proteins_renamed.fasta.gz - all unfiltered proteins as reported by MAKER's fasta_merge
Tapidor_v63_assembly.all.maker.transcripts_renamed.fasta.gz - all unfiltered transcripts
Tapidor_v63_assembly.all.maker.proteins_250bp_repeats_filtered_renamed.fasta.gz - all proteins as reported by MAKER, removed when covered for more than 50% by a RepBase repeat, or when shorter than 250 bp
Tapidor_v63_assembly.all.maker.transcripts_250bp_repeats_filtered_renamed.fasta.gz - same as above but transcripts
Tapidor_v63_assembly.all_250bp_repeats_filtered_renamed.gff.gz - same as above but gff3 file
Darmor
Files are here: CLICK
Same files as above:
Darmor_v81_assembly.fasta.gz - assembly as pseudo-molecules
Darmor_v81_assembly.all_renamed.gff.gz - unfiltered MAKER gene models
Darmor_v81_assembly.all.maker.proteins_renamed.fasta.gz
Darmor_v81_assembly.all.maker.transcripts_renamed.fasta.gz
Darmor_v81_assembly.all_250bp_repeats_filtered_renamed.gff.gz
Darmor_v81_assembly.all.maker.proteins_250bp_repeats_filtered_renamed.fasta.gz
Darmor_v81_assembly.all.maker.transcripts_250bp_repeats_filtered_renamed.fasta.gz
