Difference between revisions of "Darmor Tapidor"

From Applied Bioinformatics Group
Jump to: navigation, search
m (→‎Unfiltered annotation)
Line 1: Line 1:
 
This page collects the files for Bayer et al. <i>B. napus</i> Darmor/Tapidor genome paper
 
This page collects the files for Bayer et al. <i>B. napus</i> Darmor/Tapidor genome paper
  
−
== Annotation ==
+
== Software ==
  
−
Genes and proteins were renamed from the MAKER names to the [http://www.brassica.info/info/genome_annotation.php Brassica standard]:
+
Colinearity analysis - [http://appliedbioinformatics.com.au/download/DarmorTapidor/Colinearity_scripts.zip Colinearity_scripts.zip]
  
−
<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>
+
LASTZSorter.py [http://appliedbioinformatics.com.au/download/DarmorTapidor/LASTZSorter.py LASTZSorter.py]
  
−
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.
+
== Annotation ==
  
  
Line 13: Line 13:
  
 
[http://appliedbioinformatics.com.au/download/DarmorTapidor/Tapidor_v63_assembly.fasta.gz Tapidor_v63_assembly.fasta.gz] - assembly as pseudo-molecules
 
[http://appliedbioinformatics.com.au/download/DarmorTapidor/Tapidor_v63_assembly.fasta.gz Tapidor_v63_assembly.fasta.gz] - assembly as pseudo-molecules
−
 
−
==== Unfiltered annotation ====
 
−
 
−
As reported by the [http://www.yandell-lab.org/software/maker.html MAKER pipeline]
 
−
 
−
[http://appliedbioinformatics.com.au/download/DarmorTapidor/Tapidor_v63_assembly.all_renamed.gff.gz Tapidor_v63_assembly.all_renamed.gff.gz] - annotation in GFF format
 
−
 
−
[http://appliedbioinformatics.com.au/download/DarmorTapidor/Tapidor_v63_assembly.all.maker.proteins_renamed.fasta.gz Tapidor_v63_assembly.all.maker.proteins_renamed.fasta.gz] - predicted proteins
 
−
 
−
[http://appliedbioinformatics.com.au/download/DarmorTapidor/Tapidor_v63_assembly.all.maker.transcripts_renamed.fasta.gz Tapidor_v63_assembly.all.maker.transcripts_renamed.fasta.gz] - predicted transcripts
 
  
 
==== Filtered annotation ====
 
==== Filtered annotation ====
  
−
No AED=1 scores, no overlap with repeatmodeler output, transcripts longer than 100 bp, no Transposase domains
+
No AED=1 scores, ntranscripts longer than 100 bp, no Transposase domains
  
 
[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
 
[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
Line 35: Line 25:
  
 
=== Darmor ===
 
=== Darmor ===
−
 
−
[http://appliedbioinformatics.com.au/download/DarmorTapidor/Darmor_v81_assembly.fasta.gz Darmor_v81_assembly.fasta.gz] - assembly in pseudomolecules
 
−
 
−
==== Unfiltered annotation ====
 
−
 
−
[http://appliedbioinformatics.com.au/download/DarmorTapidor/Darmor_v81_assembly.all_renamed.gff.gz Darmor_v81_assembly.all_renamed.gff.gz] - unfiltered annotation in GFF
 
−
 
−
[http://appliedbioinformatics.com.au/download/DarmorTapidor/Darmor_v81_assembly.all.maker.proteins_renamed.fasta.gz Darmor_v81_assembly.all.maker.proteins_renamed.fasta.gz] - unfiltered predicted proteins
 
−
 
−
[http://appliedbioinformatics.com.au/download/DarmorTapidor/Darmor_v81_assembly.all.maker.transcripts_renamed.fasta.gz Darmor_v81_assembly.all.maker.transcripts_renamed.fasta.gz] - unfiltered predicted transcripts
 
−
 
  
 
==== Filtered annotation ====
 
==== Filtered annotation ====
  
−
No AED=1 scores, no overlap with repeatmodeler output, transcripts longer than 100 bp, no Transposase domains  
+
No AED=1 scores, transcripts longer than 100 bp, no Transposase domains  
  
 
[http://appliedbioinformatics.com.au/download/DarmorTapidor/Darmor_v81_assembly.all_noAED1_RepMakAll_no_RepMakOverlap_biggerequal100bp_no_transposase_renamed.gff.gz Darmor_v81_assembly.all_noAED1_RepMakAll_no_RepMakOverlap_biggerequal100bp_no_transposase_renamed.gff.gz] - filtered annotation in GFF
 
[http://appliedbioinformatics.com.au/download/DarmorTapidor/Darmor_v81_assembly.all_noAED1_RepMakAll_no_RepMakOverlap_biggerequal100bp_no_transposase_renamed.gff.gz Darmor_v81_assembly.all_noAED1_RepMakAll_no_RepMakOverlap_biggerequal100bp_no_transposase_renamed.gff.gz] - filtered annotation in GFF

Revision as of 07:47, 9 September 2016

This page collects the files for Bayer et al. B. napus Darmor/Tapidor genome paper

Software

Colinearity analysis - Colinearity_scripts.zip

LASTZSorter.py LASTZSorter.py

Annotation

Tapidor

Tapidor_v63_assembly.fasta.gz - assembly as pseudo-molecules

Filtered annotation

No AED=1 scores, ntranscripts 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

Filtered annotation

No AED=1 scores, 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

Retrieved from "https://appliedbioinformatics.com.au/Edwards/index.php?title=Darmor_Tapidor&oldid=886"