Difference between revisions of "Darmor Tapidor"

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(Annotation)
(Annotation)
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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.
 
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 <nowiki>gff3_merge -n -g</nowiki>
+
=== Tapidor ===
  
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 - all unfiltered transcripts
+
All files are here [LINK]
  
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
+
Contained are:
  
Tapidor_v63_assembly.all.maker.transcripts_250bp_repeats_filtered.fasta.gz - same as above but transcripts
+
Tapidor_v63_assembly.fasta.gz - assembly as pseudo-molecules
  
Tapidor_v63_assembly.all_250bp_repeats_filtered.gff.gz - same as above but gff3 file
+
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_rename_key.csv.gz - Stores the translation from MAKER names to <i>Brassica</i> consortium names
+
Tapidor_v63_assembly.all.maker.proteins_renamed.fasta.gz - all unfiltered proteins as reported by <nowiki>fasta_merge</nowiki>
 +
 
 +
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

Revision as of 09:13, 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.


Tapidor

All files are here [LINK]

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