I am looking for a Virus, which have 3 RNA segments in my NGS data (Cucumber mosaic Virus). I have trimmed adapters to my ngs data and I have convert my fastq files in fasta files which I have done a blastn against a virus database. This blast gave to me a results fairly confuse. It gives to me the blast of one RNA segment (RNA 1 segment )of this virus but not the remaining RNAs. I looked in my blast file the qseqid of this RNA 1 segment of this virus and I looked the segment for this qsequid 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 encapside together, so they should be together. I am sure that they are in this NGS file,
What parameters should do I change?
Thanks in advantage.