align transcriptome to genome

Question

[Kurban]

I have a transcriptome dataset of an insect,but its not a model species. So I want to align its transcriptome with the genome of Tribolium castaneum, because they belong to the same family. So could anyone give me some suggestion how could I do that?

Thanks in advance

Answer 1

[Sean Davis]

There are many RNA-seq aligners that can probably meet your needs. Pick one (I use STAR frequently). If you have transcriptome coordinates for your mapping genome, you can use that to "guide" the RNA-seq alignments. Alternatively, you can align your transcriptome once, take the discovered junctions from this first pass, and then align again using the junctions.

[Kurban]

Thanks for the good tip. and just downloaded the paper :STAR: ultrafast universal RNA-seq aligner(I think that what u have recommended). And I am hoping by aligning my specimen' transcriptome with the genome of Tribolium castaneum to find out how many transcripts could be aligned and what r those genes function in Tribolium castaneum?

I am new at this