In the following scenario: You were given short sequence reads of plant RNA obtained from a next-generation sequencing machine (fragments of 20–30 nucleotides in length). You attempt to map them back to the genome, but a significant proportion of them do not align.
The question is: give some obvious explanations why the alignment of short sequences can fail, apart from possible contamination or technical difficulties during the preparation of the RNA.
I would answer it as because reads are short, and because of introns(since it is RNA)
Another scenario: There are some indications that the problematic sequences come from an uncharacterised plant RNA virus. What would you do next? What are the specific caveats with short sequence reads?
I got the above questions, I am a computer science student doing bioinformatics, any biologist could answer it will be well appreciated