Entering edit mode
8 months ago
Takuma
▴
20
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 ?
