Find data from "GALT species", namely chicken/rabbit/sheep

[matsen]

It would be great to find some data from an organism for which we do think that gene conv is happening. This review calls these "GALT species".

An initial search reveals this:

• Apparently the chicken germline repertoire isn't well characterized, even for TCRs. This does not bode well.
• There is one HTS data set from rabbits and chickens here, from this paper. It's made using older 454 tech, which is known to have indel problems, but it gave long reads. Hopefully they included preprocessed sequences somewhere, or I can ask one of the authors. There are IMGT genes for rabbit. We should ask William Lees for advice if we go down this road-- he's great. Note that this paper also describes scripts for searching for GC events, and analyzes the frequency of GC events.

Note that the SRA isn't entirely easy to use. Ask David for help.

[matsen]

Moved to https://github.com/matsengrp/conversion/issues/8

These issues should be about code. Issues in conversion should be about data and analysis.