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.
Are these segments similar to each other or different? If you have NGS data you should ideally be using a NGS aligner. I would recommend that you try STAR, BBMap or BWA. Use just the sequence of CMV if that is all expected to be present in your data or will there be cucumber sequence as well?
These segments are different, they codify for different types of proteins. My NGS sequence is a Cyperus longus plant which have only one segment of this virus. I am going to use these programs, thanks!