Hello Irene,

Original MAF files come from UCSC at http://genome.ucsc.edu in the downloads area. In your local, you can either use this in from your history, or add it as a pre-cashed dataset to make it available to the tool group " Fetch Alignments".

To make it simple, you can rsync our version of the data. You will want the "maf_index.loc" file, found in the "location" directory (just get the whole thing and pick out what you need) and the directory "hg18". You technically want the subdirectly "hg18/align/multiz3way", but getting the reference genome will later be useful, and you also might want the various indexes. While here, also getting "panTro2" and "rheMac2" would be a good idea.

Rynch and other local data set-up help can be found here:
http://wiki.galaxyproject.org/Admin/Data%20Integration

These two publications cover how to use the various MAF manipulation tools. The individual tools also have help directly on the tool forms:
https://main.g2.bx.psu.edu/u/dan/p/maf
https://main.g2.bx.psu.edu/u/galaxyproject/p/using-galaxy-2012 (see Protocol 4)

For example, if you have a bed file of coordinates, pull the corresponding MAF blocks using tools in this group that start with names like "Stitch or Extract". The forms and examples explain the difference.

For indel analysis, look under the tool group " Regional Variation". The tool " Fetch Indels from 3-way alignments" is most likely what you are looking for.

Hopefully this helps,

Jen
Galaxy team

On 3/22/13 2:34 PM, Irene Kaplow wrote:

I would like to be able to replicate what Galaxy does to find indels on my own machine. However, I am facing the following challenges:

1. I want to find Indels in the 3-way multiz alignment of hg18, panTro2, and rheMac2, but I cannot find the alignment anywhere. Where can I get the alignment file?

2. I cannot find code for extracting the Indel's anywhere. What program did you use?

Thanks so much!

Irene
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