To decontaminate bacteria and viruses nucleotide, I am trying to perform BlobTools for assembled genome of one beetle.
In the step for generating hits files, I did diamond blastx:
diamond blastx \
--query MyAssembledGenome.fa \
--db uniprot_sprot.dmnd \
--max-target-seqs 1 \
--sensitive \
--threads 8 \
--evalue 1e-25 \
--outfmt 6 \
--out result.out
Consequently, only 4664 scaffolds were aligned against uniprot/swiss-prot database. But the MyAssembledGenome.fasta has about 55,000 scaffolds in total. Is the small number of hit scaffolds usually happened ?
And how should I treat non-hit scaffolds ? removing them for downstream analyses, such as identification of transposable element ?
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written
by
Takuma •
1 answer
You could try using a larger database such as ncbi's nr database in fasta format instead of the default format then from there diamond can add the nr database fasta files as a database.
The swissprot database can be used later for your annotations since it is more accurate.
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