Hello, I have received small RNA-seq data from a pathogenic bacteria for bioinformatic analysis. After trimming the adaptors with trim_galore, fastq file was mapped (almost 1 million reads) to the reference genome using bowtie and got overall 26% mapping rate (unique + multiple mapped). Mapping rate dose not change much even if I allow two mismatches. For negative control, reads were also mapped to mouse genome which again gives 25% mapping rate, similar to what I get when I align to the bacterial genome. Most of these mapped reads map to rRNA ans tRNAs, this is why mapping to bacterial genome and mouse genome gives similar results. Now, I do not know what are those 75% unmapped reads. It is possible that there was contamination(s) during library preparation, etc. How can I find the source of contamination? Is there a way to BLAST unmapped reads to find out which genome/strain they are probably coming from?