I'm trying to run segway (version
3.0.4), with concatenated tracks and train on a subset of coordinates.
I went through the tutorial https://segway.readthedocs.io/en/latest/quick.html and
understand the specific parts, but it seems I couldn't find some command arguments in the segway version I installed from conda. E.g. I tried to run a concatenated segmentation by separating tracks with a comma through the following command, but got the error
in orange:
segway --track h3k27me3 --track h3k36me3 --include-coords=test.bed test.genomedata traindir_track
usage: segway [global_args] COMMAND [args]...
segway: error: argument
train create a model with learned parameters
- train-init prepare initial models for parallel training
- train-run train initial models to completion criterion, in parallel
-- train-run-round train models for one round, in parallel
- train-finish select best model and prepare for `annotate`
annotate label a genome using a model
- annotate-init prepare for parallel annotation
- annotate-run annotate the genome, in parallel
- annotate-finish concatenate parallel annotation results
posterior infer posterior probabilities of each label across a genome
- posterior-init prepare for parallel posterior inference
- posterior-run infer posterior probabilities, in parallel
- posterior-finish concatenate parallel posterior inference results
Use `segway COMMAND --help` for help specific to command COMMAND.
: invalid choice: 'h3k27me3' (choose from '', 'train-init', 'train-run', 'train-finish', 'train-run-round', 'annotate-init', 'annotate-run', 'annotate-finish', 'posterior-init', 'posterior-run', 'posterior-finish',
'train', 'annotate', 'identify', 'posterior', 'identify+posterior')
Would you please help advise how to achieve that?
And separately, if I run segway with some assays in forward and reverse strand (RNA-seq) but some non-stranded ChIP-seq assays, is it ok I just duplicate the non-stranded ChIP-seq data to .forward and .reverse track, and use command like the following:
segway --track h3k27me3.forward,h3k27me3.reverse,rna.forward,rna.reverse --track brain.h3k27me3.forward,brain.h3k27me3.reverse,brain.rna.forward,brain.rna.reverse --reverse-world=1
--include-coords=test.bed test.genomedata traindir_track
Thanks a lot for your attention to this issue!
Best,
Ran