How to treat --- in functional.transcripts.fasta files for BUSCO analyses

[meixilin]

Dear DNAzoo annotation team,

Thank you for making such an amazing consortium with chromosome level assembly data. I am currently trying to compare some DNAzoo assembly with assemblies on NCBI for BUSCO analyses and have a very small question. However, I noticed that for some <genomename>functional.transcripts.fasta files, the transcripts includes -- sites which are not accepted for BUSCO.

For example, in the brydes whale annotations:

Balaenoptera_edeni_HiC.fasta_v2.functional.transcripts.fasta.gz there are lines that look like these:

>Balaenoptera_027329-RA transcript Name:"Similar to Bzw1 Basic leucine zipper and W2 domain-containing protein 1 (Rattus norvegicus OX=10116)" offset:2 AED:0.00 eAED:0.00 QI:0|-1|1|1|-1|0|1|219|268
CTATGTTGACTGGTGTTCTTCTGGCTAATGGAACACTTAATGCATCCATTCTTAATAGCC
TTTATAATGAGAATTTGGTTAAAGAAGGGGTTTCAGCAGCTTTTGCTGTAAAGCTCTTTA
AATCATGGATAAATGAAAAAGATATCAATGCAGTAGCTGCAAGTCTTCGGAAAGTCAGCA
TGGATAACAGACTGATGGAACTTTTTCCTGCCAATAAACAAAGCGTTGAACACTTCACTA
AGTATTTTACTGAGGCAGGCTTGAAAGAACTCTCAGAGTATGTTCGAAATCAGCAAACCA
TAGGAGCTCGAAAGGAACTCCAGAAAGAACTTCAAGAACAGATGTCCCGTGGTGATCCAT
TTAAGGATATAATTTTGTATGTCAAGGAGGAGATGAAAAAAAACAACATCCCAGAACCCG
TTGTCATTGGGATAGTCTGGTCCAGCGTAATGAGCACCGTGGAATGGAACAAAAAGGAAG
AGCTTGTAGCAGAGCAGGCCATCAAGCACTTGAAGCAATACAGCCCTCTACTTGCTGCCT
TTACTACTCAAGGTCAGTCTGAGCTGACTCTGTTACTGAAGATTCAGGAGTATTGCTATG
ACAACATTCATTTCATGAAAGCCTTCCAGAAAATCGTGGTGCTTTTTTATAAAGCTGAAG
TCCTGAGTGAAGAGCCCATTTTGAAGTGGTATAAAGATGCACATGTTGCAAAGGGAAAAA
GTGTCTTCCTTGAGCAAATGAAAAAGTTTGTAGAGTGGCTCAAAAATGCTGAAGAAGAAT
CTGAGTCTGAAGCTGAAGAAGTTAGGAGTAATGGA--------CCCCGGCATGGCAAACA
GTTGAAGAACGGAGAAAACTGGATAGCTGACCT-TCCAGATAGTTGTTGGCACTCAGAAC
CACC-----TCAAG-----TACA--GCCATCCAAACCAGTAATTACATTGCTGCATTATT
TCTGTGTTAACTGTGAAAT-CTG--CTGCTTGTCTGTACCCTTGAAATGGAA-TAAAATT
TC-ATG

However the - is not a valid base in the BUSCO software:

Bio.Data.CodonTable.TranslationError: Codon '-TC' is invalid

I was wondering should I remove the - (GA--------CC to GACC ) or change them to N (GA--------CC to GANNNNNNNNCC) for BUSCO compatibility?

Thank you very much in advance! And thank you for making this amazing pipeline available!

Best,
Meixi