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Downstream analysis

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evinpadhi edited this page Sep 15, 2021 · 14 revisions

Bandage plot

After running ACES, there are multiple files that will be generated that can be used in various downstream analyses. For instance the .GFA file can be viewed in Bandage (https://rrwick.github.io/Bandage/) which can give insights about the conservation of your element of interest. For an example of this see Figure 1 of the ACES manuscript.

PhastCons analysis

A second analysis that can be done is using PHAST (http://compgen.cshl.edu/phast/) to identify conserved elements within the alignment file. To do so please run the following steps after installing PHAST:

  1. Estimate a neutral model from the alignment phyloFit --EM --tree <ACES_raxml_tree>.phy -out-root <file_prefix> <ACES MSA ouput>
  2. Generate conserved and nonconserved models from the data phastCons --estimate-trees <file_prefix> <file_prefix>.mod --no-post-probs
  3. Identify conserved elements using the onserved and nonconserved models phastCons <ACES MSA ouput> <file_prefix>.cons.mod,<file_prefix>.noncons.mod > <file_prefix>_scores.bed

The final file, <file_prefix>_scores.bed, will contain the locations of conserved elements within you sequence of interest and the log odds score for that sequence being a conserved element. For detailed usage on phastCons see http://compgen.cshl.edu/phast/phastCons-HOWTO.html, this analysis here is based off option 2 from this page and estimates all parameters for the models from the data.

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