Extract Pairwise MAF Blocks

[jennaj]

Here is my prior example. I confirmed everything is still working exactly the same. Notice how I pulled in all the core data needed for this and some extra reference data most people will like to have around (consider that optional).

This should be simplified enough for students to do but please ask about any questions.

@jennaj

This is a test history with some data loading into it – query and target. https://usegalaxy.org/u/jen-galaxyproject/h/test-maf-tools-2023

It will have a reference MAF and a set of RefSeq coding exon coordinates. Both based on hg38’s chr22 to keep the test smaller but still representative. Once done, any of the MAF tools should technically work fine. Do you want to get a copy of it to play around in? If you run into a problem, share a history back. Makes it easier to troubleshoot with a real example

So, three potential solutions

1. Do the query at UCSC, and send the results to Galaxy
2. Query the index from UCSC and send that to Galaxy, then use tools in Galaxy (extract block, stitch blocks, other MAF functions)
3. Maybe more, but let us know about the mm9/mm10 question. Hg19-mm10 is possible but we do not plan to load the other pairwise data, just the N-way types of data indexes. So this option would involve the hg19 100-way I linked above. This may not be immediate, but we do want to be responsive to requests if this is something people will find useful.

And one more…

4. Use the hg38-30way hosted on the UseGalaxy servers as a native index. The species included are in the readme where the data was sourced → Index of /goldenPath/hg38/multiz30way