Can I compare RNA-Seq contigs data with genome data

[sadaharu]

Hi,

I obtained an old data of RNA-Seq contigs but without raw reads. And my boss wants me to find if those contigs can be comparable with the relative reference genome (which is annotated)

What program or strategy I should use to analyse those contigs? Maybe , I could better annotate them?

Thanks in advance!

[mastal]

You could use BLAT to align the RNA-Seq contigs to the reference genome.

https://genome.ucsc.edu/FAQ/FAQblat.html

[sadaharu]

You could use BLAT to align the RNA-Seq contigs to the reference genome.

https://genome.ucsc.edu/FAQ/FAQblat.html

Thanks a lot! Let me check it out first.

[Melissa]

Blat, provided both species are highly related (>95%). Otherwise, blast to give you an idea of your species in relation to the sequenced species. If you use blast, you will get multiple alignments to the same gene in the genome because blast can't extend alignments over the introns.