Difference between revisions of "Darmor Tapidor"

Revision as of 03:09, 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 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.

Files:

Tapidor_v63_assembly.all.gff.gz - this contains all unfiltered MAKER gene models as reported by MAKER's 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

Tapidor_rename_key.csv.gz - Stores the translation from MAKER names to Brassica consortium names