We're working with a de novo transcriptome of a non-model organism. There were some genome assemblies for it, but we decided not to use it for GE analysis since they weren't annotated and also looked suspicious in some ways. Yet we've tried to map rRNA/mitRNA filtered reads on each of them and it appeared that 7-20% of reads wouldn't map on any variant of subject genome, so it's a contamination. We've mapped unaligned reads on genomes of every organism we're also working with, but there weren't any serious match (0-1%).
What could it be? Is it for sure contamination of some kind or might be something else?
Should we still work with all reads, or
choose those which are aligned on a genome and assemble a de novo transcripts with them?
UPD: The organism is basidiomycete fungus Lentinula edodes.
I've updated the OP. How do you blast READS? There are hundreds of millions of them with the length 30-45 bp. Did you mean blasting assembled contigs?
You can use one of the faster alternatives to blast and only use it on the reads that are left over, but simply using the contigs should be good enough. In addition you can use kraken. Consider also that 80-93 %aligned is quite OK for a nomo depending on the completeNess of the genomes.
If this rate of unaligned reads is fine, am i suppose to use all reads (aligned and unaligned) in further work?