I have a data for viral RNA-seq and wonder if Bowtie should be fine. Idealy we would use ToPhat but I guess it may not work in virus as there are all exons.
Thanks for sharing the info
Thanks for sharing the info
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Indeed. Spliced alignment is not needed so bowtie or bwa should make the deal I guess. Unless of course you are looking at the expression of the host's genes. -
Viral RNA-seq
Thanks syfo,
It is human virus and I have already checked human genes, no I am concerned with only viral genes expression.
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Number of reads
Hi I would like to know if you could share the number of reads you got ailgned to the virus genome and how did you calculate the covarage. I am planning on running an RNAseq to analyse virus rna expression, but I am afraid of not getting enough number of reads.
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