dsRNA_sensing

In this project we look for antisense transcripts from an AAV cargo to show the presence of formation of dsRNA. An immune response is often associated with dsRNA. Showing the presence of these antisense transcripts could explain immune responses accompanied by AAV infection.

Step by step guide to extracting and examining the reads

1. Extract all the mapped and unmapped reads from the RNAseq bam files
2. Separate the sense and antisense reads
3. Individually count the sense and antisense reads to a custom GTF files that has annotations of the sense and antisense features
4. Quantify the counts using custom R code.