Apologies for the naive question, I was just wondering, what is generally retained from a vector sequence that is present in the RNA-seq alignments?
I would assume any genes are retained while promoters would not be? Would fluorochromes such as GFP or YFP be retained? Would intermediary regions between the promoters and gene (for example 20bp) be present as well? Is there any easy way to determine which parts are retained?
I assume you are referring to an experiment where a transgene has been introduced on a plasmid vector into cells or a plant/animal before RNA is extracted for RNAseq. RNA seq will capture all (poly-adenylated, greater than 200bp - depending on the prep method) RNA in the cell, and so will include any part of the vector that is transcribed into RNA in the cell. This will generally mean that reads from transgenes will be present - from the transcription start site, to the polyA site, minus any introns. The actual location of the TSS relative to what is annotated as the promotor, and polyA not always massively clear, and some times people do RNA seq to work this out!
While reads will be present in the data, they won't be present in the alignments unless the sequence of the transgene, or the whole vector, was included in the reference genome which the reads were aligned to.
