Getting MIRA alignments into Artemis

[Hobbe]

Hi, very new and inexperienced user here. I was thrown head-first into a genome-project, and am currently trying to figure out which programs to use to visualize results.

We have 454 data (of a fungus) that I have successfully assembled into contigs using MIRA. Artemis in combination with BamView seems to be able to visualize the alignments as well as search for ORFs and a bunch of other things, and I would like to use that program. However, I can't convert my alignments to BAM format which is needed for BamView to work. Artemis reads the fasta contigs fine, and I can check the ACE alignments in other programs like Tablet or Eagleview, but I would prefer to be able to do all of those things in one program.

So, does anyone know how I could convert ACE (or any of the other alignment outputs from MIRA) to BAM?

All help very much appreciated!

[imilne]

Why not let us (the Tablet developers) know what you'd like to be able to do and perhaps it's something that could get added to Tablet.

In the meantime, one way of getting to bam would be by using the amos tools and converting ace to afg, then afg to bank, bank to sam, then sam to bam.

(and people wonder why we try to add support for lots of file formats in Tablet... )

[Hobbe]

Thanks for the quick answer. Good to know there is a way of getting the data into Artemis, even if it would mean a number of conversions.

About what I would like to do and possibly see implemented in Tablet, I must confess I will have to get back to you about that one. Still figuring out how and what I want to do. I wanted to find the ORFs, and couldn't find that function in Tablet, but now I've realized that I don't need that anymore. Artemis still looks appealing since it allows me a good overview of an annotated genome while at the same time allowing me to check the alignments of the individual contigs. At least, that is how I understand it.

Excellent to get feedback from developers and I must say my first impressions of Tablet are very favorable. Thanks for your great work.

[jkbonfield]

It's also possible to import ACE using Gap5 and then export it back to SAM from there, but I'm not sure if it's foolproof (possibly no more or less than AMOS though) as SAM and ACE has several different concepts to battle.

Eg, ACE has read names, SAM as template names. ACE handles more than 2 reads per template, SAM has a strict maximum of two (which shouldn't be an issue for your case).

James