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ComparativeGenomicsToolkit / neutral-model-estimator

Simple pipeline to go from an alignment to a neutral model, using the PHAST toolkit
MIT License
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Installing the pipeline and question on halPhyloPTrain.py #1

Open SimonaSecomandi opened 3 years ago

SimonaSecomandi commented 3 years ago

Hello,

I'm trying to train a neutral model that I will then use to estimate PhyloP scores on my model species (Hirundo rustica), which is one of the species included in my HAL alignment generated with Cactus 1.2.3.

For the neutral model I would like to reproduce this analysis with your pipeline, but I don't know how to install it! However, I tried using halPhyloPTrain.py on ancestral repeats.

This is the command I'm using: halPhyloPTrain.py --numProc 32 --no4d --substMod REV ../../9_genomes.hal Anc0 Anc0_REPEATS_NEUTRAL_MODEL.bed Repeats_neutral_model.mod

For this command I'm using the root ancestral genome Anc0 as a reference, while for PhyloP scores I'm planning to use halPhyloPMP.py with my species (Hirundo_rustica) as a reference.

Does it sound good to you? It is correct to use the ancestral genome (from which I extracted the repeats) as a reference for training the neutral model, even if I'm interested in another species?

Many Thanks

SimonaSecomandi commented 3 years ago

Hello again, do you have any suggestions on how to install the pipeline? Many thanks again.