Open BoBo2021jenny opened 11 months ago
Hi @BoBo2021jenny
Theoretically, yes, the pipeline can perform a "chainself" if you align the reference genome against itself. However, there are some caveats:
Maybe @MichaelHiller has some insights on how to optimize this?
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
Hi I want to do chainself. Can this pipeline do chainself?