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?

  • $\begingroup$ I have edited your question. Can you please confirm if this is what you meant? Add more details; for example, length of the reads, number of reads and percentage of reads mapping to your RNA 1 segment, where are other reads mapping etc. $\endgroup$ – WYSIWYG Mar 28 '19 at 12:29
  • $\begingroup$ Also, you do not generally use BLAST for aligning short RNAseq reads. Try other NGS aligners like Bowtie or STAR (since this is a viral genome you may not need splice site aligners like HISAT). $\endgroup$ – WYSIWYG Mar 28 '19 at 12:34

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