Some examples of Intron aware aligner?

Question

[Kenny]

Hi all,

I would like to do gene annotation on my genome assembly. My PI wants me to use intron aware aligner and I found the following programs:

Apollo (http://genomearchitect.github.io/)

Rail-RNA (http://docs.rail.bio/)

Have someone used the above programs before? Do you have any other suggestions?

I am new in this field, any help will be appreciated!

Kenny

[WouterDeCoster]

It's unclear which data you exactly have and what you aim to obtain, please elaborate.

[Kenny]

I have a scaffold genome and transcriptome of an organism. I have blast the transcriptome against the genome. When I checked the blast output, for example, one transcript appears in different scaffolds. Another example, one transcript appear in the same scaffold but there are gaps. I guess there might be an intron there. Therefore, I would like to visualize the genome and transcriptome to find out.

Hope I make this a bit clear.

[GenoMax]

If you are only looking to align a transcriptome against a genome/scaffold then take a look at GMAP.

Answer 1

[Puli Chandramouli Reddy]

Hi,

If you want to map or align transcripts to genome then you can use Exonerate or NUCMER or BLAT.