For 1, you likely do not need to perform any normalization. Segway by default does an arcsinh normalization on each track (which can be turned off). Additionally, the conditional probability distribution learned is specific to the track and is evenly weighted
across all tracks.
For 2, there is no good way of attempting multiple labels in one command. Multiple instances of training are focused on finding the best fit for a given number of labels with different initial stating parameters. If you want to try different label numbers you
need to produce a new trained segway model for each one.
Hope that helps.
Eric
Hi Eric,
Sorry to interrupt you again, I have two more questions on running segRNA:
- For RNA-seq data, what type of data normalization should we perform before running segRNA? Also, does it have to be consistent with other ChIP-seq assay data distributions when running segway jointly on RNA-seq and ChIP-seq?
- I was trying to specify "num-labels" to multiple values so that the model can try different number of clusters at once, but go the following error:
-
segway train --num-labels=2:4:1 test.genomedata traindir_nlabel
sh: -c: line 0: syntax error near unexpected token `('
sh: -c: line 0: `x86_64-conda_cos6-linux-gnu-c++ -E -x assembler-with-cpp -DCARD_SEG=slice(2, 4, 1) -DCARD_SUBSEG=1 -DCARD_FRAMEINDEX=2000000 -DSEGTRANSITION_WEIGHT_SCALE=1.0 -Itraindir_nlabel
-I. traindir_nlabel/segway.str'
Unexpected EOF Error: expecting GM magic keyword at line 1
Exiting Program
Would you please advise on how to fix it? Thanks a lot for your attention on this!
Thanks,
Ran
Hi,
You're simply missing the "command" part of the arguments. This is usually "train" or "annotate". In this case, it looks like you are missing "train".
I believe the idea behind the non-stranded data is correct.
Hope that helps!
Eric
Dear Eric,
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
Yes but you will probably want to duplicate the non-strand-specific data like ChIP-seq in both the forward and reverse worlds.
Dear Roberts and Michael,
Thanks for the pointer! Since we have multiple assay types (ChIP-seq, RNA-seq, etc), can we use SegRNA for ChIP-seq assays together with RNA-seq?
Best,
Ran
This is the relevant section in the docs about the --reverse-world option and concatenation.
Not sure why it didn't come up in the search!
Eric
[Bcc Bill]
Eric can you please help with this? M
Michael, I am not sure which documents you are referring to. I searched the readthedocs for Segway for "reverse-world" but came up empty:
Can you help?
Thanks.
Bill
Yeah unfortunately if we let anyone send to it the spam is out of control.
We have a preprint on SegRNA in fact! The - - reverse-world option is what you need, should be described in the docs.
Michael
Hi Michael,
I tried to figure out how to send a support message about Segway, but it seems like I can't ask a question without subscribing to the list. Is that right? Seems like a lot of overhead!
Anyway, the question (below) is whether RNA-seq is supported. Did you ever end up implementing the two-strand stuff for RNA-seq analysis?
Thanks!
Bill
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From: William Stafford Noble <
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To:
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Cc:
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Date: Wed, 1 Jun 2022 20:39:03 -0700
Subject: RNA-seq segmentation
Does Segway support RNA-seq segmentation? I know there were plans to do so, but I don't know (remember?) whether those plans were ever completed. We have data from four tissues and five assay types, and we were thinking of applying Segway to it, but
one of the assays is RNA-seq.
Thanks.
Bill
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