I would like to ask you. Any of you has used RATT tool for annotation transfer of assemblies?
I followed each step described by its documentation and prepared embl file of each scaffold in the reference assembly, and put them in a directory.
But RATT gave an error below; I am using the reference Species1.fa. Please make sure that the description line of each fasta entry is the same than in the embl file name!
should be the same name as the embl file in embl
CERROR: Could not parse delta file, nucmer.test.delta error no: 400
in my embl directory:
there are embl files of each scaffold in the reference fasta like these:
scaffold00001 scaffold00203.embl scaffold00452.embl scaffold00744.embl scaffold01202.embl scaffold02167.embl
and an embl file:
ID scaffold00002; SV 1; linear; genomic DNA; HTG; INV; 1055470 BP. FH Key Location/Qualifiers FH FT CDS complement(join(127801..127891,127164..127423,126853..127105,126737..126771)) FT /systematic_id="gene_id 0 ; sequence KOG3106.9 ; gene_orientation +" FT /colour=7 SQ Sequence 1055470 BP; 349924 A; 176034 C; 176072 G; 346086 T; 7354 other; ATTATCGAGT TCCCACATTT TCTCCTCTTC TTTTTGTACA TGATGTATAC ATCTTTGCCA 60
How to run RATT successfully ?