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0xTCG / biser

A fast tool for detecting and decomposing segmental duplications in genome assemblies
MIT License
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Cannot modify the max error value when running biser #28

Closed yangyxt closed 1 year ago

yangyxt commented 1 year ago

image

inumanag commented 1 year ago

Hi @yangyxt

Which version of BISER you are using? This is only supported in the latest version.

yangyxt commented 1 year ago

@inumanag Thanks for the response.

I just managed to build biser from github and package it into a docker image: https://hub.docker.com/repository/docker/yangyxt/biser/general

By far, I have several inquiries regarding the latest version:

  1. what are the scores referring to in the result table, whats the specific calculation of it ?
  2. Can we have a decomposed SD binary map ? With a metric stat their similarity ?
  3. Can we have further explanation about how the arguments values help control the decomposition of the SD intervals?

Much appreciated!

inumanag commented 1 year ago
  1. Which scores? The explanation is outlined in the README; if it is not clear, please tell me which needs further clarification.
  2. I do not understand what would that be, but in either case, it's unlikely that I will be able to add a major feature for the time being. Would be happy to accept PRs, though.
  3. Currently, decomposition is not parametrizable by an end-user. You will have to tweak https://github.com/0xTCG/biser/blob/master/biser/codon/decompose.codon for that; some parametrization experiments are done here: https://dspace.library.uvic.ca/handle/1828/13343, but for more details, you will have to tune the parameters yourself.