Entering edit mode
2.8 years ago
Susan
•
0
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.
One approach would be based on raw count of RNA-seq reads mapped to your genes: no reads mapped = no expression detected.