This is the code to reproduce the DNAzoo genome annotations.
macmanes-lab / dnazoo_annotation Goto Github PK
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License: GNU General Public License v3.0
This is the code to reproduce the DNAzoo genome annotations.
License: GNU General Public License v3.0
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
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