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