Take RNASeq data and find number of viral transcripts of specific virus
I've been browsing BioStar, and I wasn't able to find a concise explanation beforehand, so apologies if this is redundant.
I want to take RNA sequencing fastq's, and then find the number of viral transcripts that are mapped to a specific viral genome such as EBV.
I was planning on using STAR to align the fastq and htseq to count the transcripts.
- How should I use STAR to map the fastq's to the viral genome? Will I need to use a virus specific .gtf file? Will I need to create a star index for the viral genome as well?
- Is this a valid/good approach or should I be thinking about this in a different way?
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Use VirDetect. It uses
STARand should walk you through steps of doing what you are asking for.Thanks for the reply - this seems really helpful.