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Mapping transcriptomes against each other to find genetic differences

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!

rna-seq sequence r assembly
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written by julianneradford • julianneradford

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.

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written by karl.stamm karl.stamm

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.

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written by julianneradford • julianneradford

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