Difference between revisions of "Darmor Tapidor"

Revision as of 04:05, 26 April 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

Tapidor_v63_assembly.fasta.gz - assembly as pseudo-molecules

Unfiltered annotation

As reported by the MAKER pipeline

Tapidor_v63_assembly.all_renamed.gff.gz - annotation in GFF format

Tapidor_v63_assembly.all.maker.proteins_renamed.fasta.gz - predicted proteins

Tapidor_v63_assembly.all.maker.transcripts_renamed.fasta.gz - predicted transcripts

Filtered annotation

No AED=1 scores, no overlap with repeatmodeler output, transcripts longer than 100 bp, no Transposase domains

Tapidor_v63_assembly.all_noAED1_RepMakAll_no_RepMakOverlap_biggerequal100bp_no_transposase_renamed.gff.gz - filtered predicted annotation in GFF format

Tapidor_v63_assembly.all.maker.transcripts_noAED1_RepMakAll_no_RepMakOverlap_biggerequal100bp_no_transposase_renamed.fasta.gz - filtered predicted transcripts

Tapidor_v63_assembly.all.maker.proteins_noAED1_RepMakAll_no_RepMakOverlap_biggerequal100bp_no_transposase_renamed.fasta.gz - filtered predicted proteins

Darmor

Darmor_v81_assembly.fasta.gz - assembly in pseudomolecules

Unfiltered annotation

Darmor_v81_assembly.all_renamed.gff.gz - unfiltered annotation in GFF

Darmor_v81_assembly.all.maker.proteins_renamed.fasta.gz - unfiltered predicted proteins

Darmor_v81_assembly.all.maker.transcripts_renamed.fasta.gz - unfiltered predicted transcripts

Filtered annotation

No AED=1 scores, no overlap with repeatmodeler output, transcripts longer than 100 bp, no Transposase domains

Darmor_v81_assembly.all_noAED1_RepMakAll_no_RepMakOverlap_biggerequal100bp_no_transposase_renamed.gff.gz - filtered annotation in GFF

Darmor_v81_assembly.all.maker.proteins_noAED1_RepMakAll_no_RepMakOverlap_biggerequal100bp_no_transposase_renamed.fasta.gz - filtered predicted proteins

Darmor_v81_assembly.all.maker.transcripts_noAED1_RepMakAll_no_RepMakOverlap_biggerequal100bp_no_transposase_renamed.fasta.gz - transcripts