Generating Hits files for BlobTools

Question

[Takuma]

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 ?

Answer 1

[jtorre28]

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.