Dear All,

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!

>scaffold00001

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 ?

Thank you