UCSC Custom Genomes

[puggie]

Dear Forum Members,

I have not been able to find the answer to my questions on the forum.

What I want to do is load Bam files into UCSC (I can manage that). However, if I have Bam files aligned to a custom genome, e.g. some extraction of a chromsome with additional sequence added and so on (i.e. not available in UCSC), I will not load? How do I import my own genome into UCSC?

My apologies if this is "too" trivial, however, I'm a newbie still.

[GenoMax]

Is the UCSC import needed for a specific reason? You could always set up a local install of the UCSC browser and set up your custom genome there but that would mean a lot of additional work.

Alternatively, you can take the easy way out and use a different genome viewer like IGV instead.

[puggie]

Is the UCSC import needed for a specific reason? You could always set up a local install of the UCSC browser and set up your custom genome there but that would mean a lot of additional work.

Alternatively, you can take the easy way out and use a different genome viewer like IGV instead.

Yes, it is for illustration purposes. Dont like pictures of IGV. Will it only be possible on local install?

[GenoMax]

I was going to suggest "trackster" visualization tool in galaxy but you are not going to be able to export the graphics (except as a "screenshot").

You could also try IGB: http://bioviz.org/igb/index.html

What do you not like about IGV (export options/just the look)?