Difference between revisions of "Darmor Tapidor"

Revision as of 09:24, 7 March 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

All files are here CLICK

Contained are:

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 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