I'm trying to reproduce this analysis https://github.com/ComparativeGenomicsToolkit/neutral-model-estimator , which uses the repetitive regions of the ancestral genome of the lineage of interest to build a neutral model. However, I tried to performe the pipeline step by step and the halPhyloPTrain.py script returns to me an error. It requires a BED12 input files with an exon annotation of the genome of interest. How can I use this script with ancestral repeats?
Hi all,
I'm trying to reproduce this analysis https://github.com/ComparativeGenomicsToolkit/neutral-model-estimator , which uses the repetitive regions of the ancestral genome of the lineage of interest to build a neutral model. However, I tried to performe the pipeline step by step and the halPhyloPTrain.py script returns to me an error. It requires a BED12 input files with an exon annotation of the genome of interest. How can I use this script with ancestral repeats?
Many thanks,
Simona