Difference between revisions of "Darmor Tapidor"
Philippbayer (talk | contribs) |
Philippbayer (talk | contribs) (→Annotation) |
||
| Line 13: | Line 13: | ||
| − | All files are here [ | + | All files are here [download/Tapidor_Assembly_with_Annotations.tar.gz CLICK] |
Contained are: | Contained are: | ||
| Line 34: | Line 34: | ||
=== Darmor === | === Darmor === | ||
| − | + | ||
| + | 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 | ||
Revision as of 09:20, 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 [download/Tapidor_Assembly_with_Annotations.tar.gz 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
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
