Difference between revisions of "Darmor Tapidor"

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(→‎Tapidor)
(→‎Tapidor)
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=== Tapidor ===
 
=== Tapidor ===
 +
 +
[http://appliedbioinformatics.com.au/download/DarmorTapidor/Tapidor_v63_assembly.fasta.gz Tapidor_v63_assembly.fasta.gz] - assembly as pseudo-molecules
 +
 +
==== Unfiltered annotation ====
 +
 +
Tapidor_v63_assembly.all.maker.proteins_renamed.fasta.gz
  
  
  
−
[http://appliedbioinformatics.com.au/download/DarmorTapidor/Tapidor_v63_assembly.fasta.gz Tapidor_v63_assembly.fasta.gz] - assembly as pseudo-molecules
+
Tapidor_v63_assembly.all.maker.transcripts_renamed.fasta.gz
 +
 
 +
Tapidor_v63_assembly.all_renamed.gff.gz
  
−
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_v63_assembly.all.maker.proteins_renamed.fasta.gz - all unfiltered proteins as reported by MAKER's <nowiki>fasta_merge</nowiki>
+
==== Filtered annotation ====
  
−
Tapidor_v63_assembly.all.maker.transcripts_renamed.fasta.gz - all unfiltered transcripts
+
No AED=1 scores, no overlap with repeatmodeler output, transcripts longer than 100 bp, no Transposase domains
  
−
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
+
[http://appliedbioinformatics.com.au/download/DarmorTapidor/Tapidor_v63_assembly.all_noAED1_RepMakAll_no_RepMakOverlap_biggerequal100bp_no_transposase_renamed.gff.gz 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_250bp_repeats_filtered_renamed.fasta.gz - same as above but transcripts
+
[http://appliedbioinformatics.com.au/download/DarmorTapidor/Tapidor_v63_assembly.all.maker.transcripts_noAED1_RepMakAll_no_RepMakOverlap_biggerequal100bp_no_transposase_renamed.fasta.gz Tapidor_v63_assembly.all.maker.transcripts_noAED1_RepMakAll_no_RepMakOverlap_biggerequal100bp_no_transposase_renamed.fasta.gz] - filtered predicted transcripts
  
−
Tapidor_v63_assembly.all_250bp_repeats_filtered_renamed.gff.gz - same as above but gff3 file
+
[http://appliedbioinformatics.com.au/download/DarmorTapidor/Tapidor_v63_assembly.all.maker.proteins_noAED1_RepMakAll_no_RepMakOverlap_biggerequal100bp_no_transposase_renamed.fasta.gz Tapidor_v63_assembly.all.maker.proteins_noAED1_RepMakAll_no_RepMakOverlap_biggerequal100bp_no_transposase_renamed.fasta.gz] - filtered predicted proteins
  
 
=== Darmor ===
 
=== Darmor ===

Revision as of 03:42, 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

Tapidor_v63_assembly.all.maker.proteins_renamed.fasta.gz


Tapidor_v63_assembly.all.maker.transcripts_renamed.fasta.gz

Tapidor_v63_assembly.all_renamed.gff.gz


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

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

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