RATT: annotation transfer tool

Question

[Mehmet]

Dear all,

I need to transfer annotations from v1.0 assembly to v.2.0 of the same species. I checked tools and found that RATT tool is suitable for this work. But in documentation file of RATT it says that in the embl directory there must be embl files of each scaffold of V.1.0 assembly, and V1.0 assembly has ~1200 scaffold.

Any idea on how to generate embl file of each scaffold?

In a blog (avrilomics) (http://avrilomics.blogspot.com.tr/2013/02/using-ratt-to-transfer-gene-predictions.html) I saw a perl script named gff-to-embl.pl and I tried to run it, but it gave an error:

ERROR: test_read_scaffold_lengths: cannot open new/tmp0.928503855903731

Thank you

Answer 1

[Sej Modha]

If you have the file in genbank format then you can use readseq for format conversions.