viral RNA-seq

[honey]

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

[syfo]

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.

[honey]

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.

Honey

[Lucas_USP]

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.

Thanks