Hello, It is my first using of MALT.
I ran malt-build with all refseq bacteria genomes with mapping file --acc2taxonomy megan-nucl-Jan201.db
malt-run with ancient reads with such flags -id 85 -m BlastN -at SemiGlobal -top 1 -supp 0.01 -mq 100. open .rma6 file in Megan desktop, click at the species, then File --> Extract Reads
I got .fasta file with reads that assigned to the species.
Then I decided to validate this assignments. I’ve taken ID of the reference from .blast file (also download after clicking at the specie) and run BWA: bwa aln ref_index extracted_reads_from_megan.fasta > result.bwa
bwa samse ref_index result.bwa extracted_reads_from_megan.fasta > result.sam
And there are no hits in samtools flagstat. Then I tested with reference genome of this species from Refseq and also there are no hits. Should I have more strict parameters with build-run? When I tried to blastn some of these reads on the site, it showed the hits with [Eukaryotic synthetic construct chromosome 20]. The reads for malt-run was from unmapped of human. What could be the mistake?
A lot of thanks, Valery