Difference between revisions of "Darmor Tapidor"
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== Annotation == | == Annotation == | ||
| − | Genes and proteins were renamed from the MAKER names to the [ | + | Genes and proteins were renamed from the MAKER names to the [http://www.brassica.info/info/genome_annotation.php 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 BnaC04g31330.2D for Darmor "new version" (of this paper), or BnaC04g31330.1T for Tapidor (first version) | ||
| + | |||
| + | Files: | ||
Tapidor_v63_assembly.all.gff.gz - this contains all unfiltered MAKER gene models as reported by <nowiki>gff3_merge -n -g</nowiki> | Tapidor_v63_assembly.all.gff.gz - this contains all unfiltered MAKER gene models as reported by <nowiki>gff3_merge -n -g</nowiki> | ||
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Tapidor_v63_assembly.all.maker.proteins.fasta.gz - all unfiltered proteins as reported by <nowiki>fasta_merge</nowiki> | Tapidor_v63_assembly.all.maker.proteins.fasta.gz - all unfiltered proteins as reported by <nowiki>fasta_merge</nowiki> | ||
| − | Tapidor_v63_assembly.all.maker.transcripts.fasta.gz - | + | Tapidor_v63_assembly.all.maker.transcripts.fasta.gz - all unfiltered transcripts |
Tapidor_v63_assembly.all.maker.proteins_250bp_repeats_filtered.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.proteins_250bp_repeats_filtered.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 | ||
Revision as of 01:59, 7 March 2016
This page collects the files for
Assemblies
Tapidor
pseudo-molecules collections of contigs
Darmor
pseudo-moleculues collections of contigs
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 BnaC04g31330.2D for Darmor "new version" (of this paper), or BnaC04g31330.1T for Tapidor (first version)
Files:
Tapidor_v63_assembly.all.gff.gz - this contains all unfiltered MAKER gene models as reported by gff3_merge -n -g
Tapidor_v63_assembly.all.maker.proteins.fasta.gz - all unfiltered proteins as reported by fasta_merge
Tapidor_v63_assembly.all.maker.transcripts.fasta.gz - all unfiltered transcripts
Tapidor_v63_assembly.all.maker.proteins_250bp_repeats_filtered.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.fasta.gz - same as above but transcripts
Tapidor_v63_assembly.all_250bp_repeats_filtered.gff.gz - same as above but gff3 file
