self chains

[BoBo2021jenny]

Hi I want to do chainself. Can this pipeline do chainself?

[kirilenkobm]

Hi @BoBo2021jenny

Theoretically, yes, the pipeline can perform a "chainself" if you align the reference genome against itself. However, there are some caveats:

• Most of the alignments would point to the exact same coordinates, which is essentially a waste of computational resources.
• You'll end up with a bulk of redundant information that's not particularly useful. So, in its current state, I wouldn't recommend using the pipeline for this purpose. However, it's theoretically possible to tweak it to make it more efficient for "chainself" alignments. I'm going to pin this issue, so it'll be on our sort of "to-do list" for future improvements.

Maybe @MichaelHiller has some insights on how to optimize this?

[MichaelHiller]

Our pipe is not build for self chains. But you could likely adjust it. I think lastz has a -self parameter to only expect 1 fasta and ignore the trivial alignments. Likely downstream tools also need a parameter to tell them about self alignments.

Pls have a look at https://genomewiki.ucsc.edu/index.php?title=Same_species_lift_over_construction UCSC has a blat based pipeline, which could be interesting. And this https://genomewiki.ucsc.edu/images/d/d3/SameSpeciesChainNet.sh.txt