I am looking at RNAseq data and mapping them to 3 RNA segments from Cucumber Mosaic Virus.
I trimmed the adapters from the fastq files and converted them to fasta, which I searched against a virus database using BLASTN.
The results were confusing:
The reads align to one RNA segment (RNA 1 segment) of this virus but not the other segments. I looked in my BLAST result file the qseqid of this RNA segment of this virus and compared with the ids in my fasta file.
I copied this sequence and I did a NCBI BLAST which gave to me the same result. These 3 segments are in the capsid together, so they should be together. I am sure that they are in this NGS file.
What parameters should do I change?