My honours thesis project aims to find genetic variation (or lack of) between termite populations (one invasive, one native, and one intermediate). I have 9 transcriptome termite libraries (3 locations x 3 castes), but do not have a reference assembly. I have tried to map the libraries to a closely related species, and also to Drosophila using BaseSpace Illumina RNA-Seq Alignment. The RNA-Seq Analyses I have tried to run eventually get aborted ~5 hours in (my fastq files are properly formatted, and everything is named correctly). I am wondering if you can please help me understand the issue I might be having with the RNA-Seq App or if you have any suggestions on how I can accomplish my overall goal without mapping the libraries to a reference (i.e. is there a way to map them to each other).
Thanks!
Building a reference genome for a species that doesn't have one is a pretty big task for an 'honors thesis project'. Further, using it for a three-way differential expression analysis is another big complicated project. Good luck!
Building a genome from RNA-Seq is yet another difficult task.
Maybe you want reference-free methods, or identify a few genes and just compare them, rather than a full genome-wide analysis. Lots of options now.
I have a list of genes that I want to compare as opposed to doing the genome-wide analysis. Is it possible to compare them without an annotation? If so, do you have any ideas on what tools I can use to do this?
Thanks.