Checking for gene expression in transcriptome - 1 sample RNASeq

Question

[Susan]

Dear all,

I am looking for suggestions on how to tackle the following - I currently have 1 sample RNA-Seq from 1 tissue (I assembled the transcriptome using Trinity to use for MAKER annotation). Annotation of my genome is in progress, however, I currently also have information on the closest transposable elements to my preliminary annotated genes - a list of TEs 1-2 kb close to the annotated genes. I am interested in how to approach checking if some of these preliminary annotated genes are expressed or not just using my 1 sample transcriptome data (the hypothesis is that very closely situated TEs can interfere with expression). Any suggestions on literature would be very appreciated.

[alex.zaccaron]

One approach would be based on raw count of RNA-seq reads mapped to your genes: no reads mapped = no expression detected.