Hi,
I have Illumina RNA sequencing data for viral infection only or viral treated. I would quantify the viral gene expression, but the total reads counts is various between library. Please see fig. I am wondering do I need to downsample the total reads to 5 M or is it ok to quantify using the total viral mapped reads ?? Thanks in advance
Hello! So what was the total number of reads you tried to align? Also, you should have some measure of the RNA quality. The accepted standard is the RIN, from a Aglient bioanalyzer, whihc should be above 7.0. Usually the raw data can be run through a program called FastQC and this will give you additional quality information. If you don't see anything from this that the data is poor quality, then you can use the R/Bioconductor program 'edgeR' and use the "FilterByExpr" function, section 2.7 page 14. I'll post the URL for edgeR user guide below. Good luck!!
https://bioconductor.org/packages/release/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf
Great, thanks for your answer. But the viral genes have different lengths. I am wondering if I use the EDgR package. It will not take into consideration these differences. Thanks in advance