Only Running etandem on Specific Portions of an Entire Chromosome


I work in an undergraduate research lab and we have been looking to streamline the process of using etandem for new students to reduce the likelihood of errors when manually determining the position of repeats within a chromosome. For example, currently students enter the gene of interest into etandem and find repeats, then must map each repeat among the chromosome they are within to find the exact base that the repeat begins at. It isn’t complicated but introduces some chance of error. In an attempt to remedy this, we came up with the idea of importing an entire chromosome of interest for common use and having students run etandem on specific segments of interest to find repeats only in specific portions. Up importing a chromosome from UCSC, there seems to be no way to instruct etandem to search for repeats in a specific region of the uploaded sequence. Is there some other place/setting to allow this within Galaxy? The only etandem settings we can see are repeat size range, threshold score, allow N as mismatch, allow uniform consensus and output report file format.

Thank you!

Most Galaxy tools focus on doing a specific task, which would be repeat finding for etandem. If you have a list of region on your chromosome of interest you can use
to extract a part of the fasta file and use only that part in etandem. This means you can also skip importing chromosomes from ucsc and just use what is already available in Galaxy if you’re using one of the standard model organisms.