<p>I have used <code>tophat2</code> to map rna-seq reads to a draft genome. The alignment percentage is around 75-80% for all samples. When I take the unmapped reads and blast them, they hit the same organism, indicating the unmapped reads might have potential information. How do I deal with the unmapped reads and include them in DE analysis or any other downstream analysis ? Should I go with entirely different pipeline like <code>trinity</code> ?</p>

<p>I have tried STAR and the mapping percentage increased up to 90-92% ( with tophat2, it was only up to 75-85%). I will try BBMap soon.</p>
