Question: Blast wrong, RNA seq
gravatar for apl00028
5 weeks ago by
apl000280 wrote:

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.

virus rna-seq ngs • 199 views
ADD COMMENTlink modified 1 day ago by Biostar ♦♦ 20 • written 5 weeks ago by apl000280

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?

ADD REPLYlink written 5 weeks ago by genomax64k

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!

ADD REPLYlink written 5 weeks ago by apl000280
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