Print

Print


Unfortunately I've tried for the past few days to recreate a Python 2 environment for segtools and I'm having significant difficulty. I was hoping to recreate this issue in some fashion soon.

A low hanging fruit which might solve some of your issues is to install a much later version of Genomedata. Version 1.3.6 is very old. The error reported is correct for all genomedata archives - there is no "dirty" attribute for the supercontig, but there is for the parent chromosome however. Trying to track down this issues on much older versions of Genomedata is probably not very productive.

I'll try to see if I can get an environment setup sooner than later to see if I can investigate this. Alternatively I can look into just porting over this tool to Python 3. Hopefully at least you might be able to plot your distribution manually as well.

Eric

From: ranz0 <[log in to unmask]>
Sent: Friday, July 22, 2022 5:39 PM
To: Roberts, Eric <[log in to unmask]>; segway-l: Discussion of Segway genome annotation software <[log in to unmask]>
Subject: Re: [External] Re: Rejected posting to [log in to unmask]
 
Hi Eric, 

I'm just checking in in case you missed the previous email (I realize my question is very hidden in that email).
I made sure "chr1" is in genomedata archive, and run segtools-signal-distribution (I am using python 2.7 for segtools since it seems python 3 cannot do some functions). There are four segway segmentation files (each using one tissue), I tried only using one file for now and got the following error:
  1. segtools-signal-distribution test_mod_identifydir/segway.0.bed test/chr1.genomedata

    INFO:Note: NumExpr detected 36 cores but "NUMEXPR_MAX_THREADS" not set, so enforcing safe limit of 8.

    INFO:NumExpr defaulting to 8 threads.

    INFO:Loading Segmentation from file: test_mod_identifydir/segway.0.bed

    INFO:  Parsing lines from bed format

    INFO:Loading finished in 121.5 seconds.

    INFO:Generating signal distribution histograms

    Traceback (most recent call last):

      File "/net/noble/vol1/home/ranz0/bin/anaconda3/envs/py2/bin/segtools-signal-distribution", line 10, in <module>

        sys.exit(main())

      File "/net/noble/vol1/home/ranz0/bin/anaconda3/envs/py2/lib/python2.7/site-packages/segtools/signal_distribution.py", line 390, in main

        validate(bedfilename, genomedatadir, outdir, **kwargs)

      File "/net/noble/vol1/home/ranz0/bin/anaconda3/envs/py2/lib/python2.7/site-packages/segtools/signal_distribution.py", line 281, in validate

        verbose=verbose)

      File "/net/noble/vol1/home/ranz0/bin/anaconda3/envs/py2/lib/python2.7/site-packages/segtools/signal_distribution.py", line 99, in from_segmentation

        for chromosome in chromosomes:

      File "/net/noble/vol1/home/ranz0/bin/anaconda3/envs/py2/lib/python2.7/site-packages/genomedata-1.3.6-py2.7.egg/genomedata/__init__.py", line 169, in __iter__

        yield self[groupname]

      File "/net/noble/vol1/home/ranz0/bin/anaconda3/envs/py2/lib/python2.7/site-packages/genomedata-1.3.6-py2.7.egg/genomedata/__init__.py", line 203, in __getitem__

        res = Chromosome(self.h5file, where="/" + name)

      File "/net/noble/vol1/home/ranz0/bin/anaconda3/envs/py2/lib/python2.7/site-packages/genomedata-1.3.6-py2.7.egg/genomedata/__init__.py", line 558, in __init__

        if attrs.dirty:

      File "/net/noble/vol1/home/ranz0/bin/anaconda3/envs/py2/lib/python2.7/site-packages/tables/attributeset.py", line 305, in __getattr__

        "'%s'" % (name, self._v__nodepath))

    AttributeError: Attribute 'dirty' does not exist in node: '/supercontig_0'

Would appreciate your feedback on which is the right way to do it.

Thanks,
Ran

From: ranz0 <[log in to unmask]>
Sent: Tuesday, July 19, 2022 1:15 PM
To: Roberts, Eric <[log in to unmask]>; segway-l: Discussion of Segway genome annotation software <[log in to unmask]>
Subject: Re: [External] Re: Rejected posting to [log in to unmask]
 
Hi Eric, 

Thanks for your quick response!
The solution to 2 works! I double checked chr1 is in genomedata archive:
>>> with Genome(gdfilename) as genome:
...     chromosome = genome["chr1"]
...     data = chromosome[100000:100050, 0:3]
...     print(data)
...
[[nan nan nan]
 [nan nan nan]
 [nan nan nan]

And it seems even if we don't specify the chromosome, we get another error (see my previous email). Would you please advice on that?

Thanks a lot!
Ran

From: Roberts, Eric <[log in to unmask]>
Sent: Tuesday, July 19, 2022 12:11 PM
To: ranz0 <[log in to unmask]>; segway-l: Discussion of Segway genome annotation software <[log in to unmask]>
Subject: Re: [External] Re: Rejected posting to [log in to unmask]
 
For 1, you should manually ensure that the chromosome name 'chr1' name exists in your genomedata archive through the python interface as you've demonstrated below.

For 2, you are attempting to access the genomedata archive outside of its context handler in the python interpreter and therefore running into the assertion error. If you code this as a script it should work, or skip the context handler altogether and not use the with‚Äč statement if you want to do a quick check.

Hope that helps!

Eric


From: ranz0 <[log in to unmask]>
Sent: Tuesday, July 19, 2022 2:57 AM
To: Roberts, Eric <[log in to unmask]>; segway-l: Discussion of Segway genome annotation software <[log in to unmask]>
Subject: Re: [External] Re: Rejected posting to [log in to unmask]
 
Hi Eric,

Sorry to bother you again! I am trying to summarize genomedata track values regarding to each segmentation. I tried two ways but each of them return some issue:
  1. segtools-signal-distribution (I am using python 2.7 for segtools since it seems python 3 cannot do some functions). There are four segway segmentation files (each using one tissue), I tried only using one file for now and got the following error: 
  2. segtools-signal-distribution -c chr1 test_mod_identifydir/segway.0.bed test/chr1.genomedata

    INFO:Note: NumExpr detected 36 cores but "NUMEXPR_MAX_THREADS" not set, so enforcing safe limit of 8.

    INFO:NumExpr defaulting to 8 threads.

    INFO:Loading Segmentation from file: test_mod_identifydir/segway.0.bed

    INFO:  Parsing lines from bed format

    INFO:Loading finished in 121.7 seconds.

    INFO:Generating signal distribution histograms

    ['chr1']

    Genome('test/chr1.genomedata')

    Traceback (most recent call last):

      File "/net/noble/vol1/home/ranz0/bin/anaconda3/envs/py2/bin/segtools-signal-distribution", line 10, in <module>

        sys.exit(main())

      File "/net/noble/vol1/home/ranz0/bin/anaconda3/envs/py2/lib/python2.7/site-packages/segtools/signal_distribution.py", line 390, in main

        validate(bedfilename, genomedatadir, outdir, **kwargs)

      File "/net/noble/vol1/home/ranz0/bin/anaconda3/envs/py2/lib/python2.7/site-packages/segtools/signal_distribution.py", line 281, in validate

        verbose=verbose)

      File "/net/noble/vol1/home/ranz0/bin/anaconda3/envs/py2/lib/python2.7/site-packages/segtools/signal_distribution.py", line 95, in from_segmentation

        chromosomes = [genome[chrom] for chrom in chroms]

      File "/net/noble/vol1/home/ranz0/bin/anaconda3/envs/py2/lib/python2.7/site-packages/genomedata-1.3.6-py2.7.egg/genomedata/__init__.py", line 209, in __getitem__

        raise KeyError("Could not find chromosome: %s" % name)

    KeyError: 'Could not find chromosome: chr1'


  3. Or if I don't define chromosome, I got a different error: 
  4. segtools-signal-distribution test_mod_identifydir/segway.0.bed test/chr1.genomedata

    INFO:Note: NumExpr detected 36 cores but "NUMEXPR_MAX_THREADS" not set, so enforcing safe limit of 8.

    INFO:NumExpr defaulting to 8 threads.

    INFO:Loading Segmentation from file: test_mod_identifydir/segway.0.bed

    INFO:  Parsing lines from bed format

    INFO:Loading finished in 121.5 seconds.

    INFO:Generating signal distribution histograms

    Traceback (most recent call last):

      File "/net/noble/vol1/home/ranz0/bin/anaconda3/envs/py2/bin/segtools-signal-distribution", line 10, in <module>

        sys.exit(main())

      File "/net/noble/vol1/home/ranz0/bin/anaconda3/envs/py2/lib/python2.7/site-packages/segtools/signal_distribution.py", line 390, in main

        validate(bedfilename, genomedatadir, outdir, **kwargs)

      File "/net/noble/vol1/home/ranz0/bin/anaconda3/envs/py2/lib/python2.7/site-packages/segtools/signal_distribution.py", line 281, in validate

        verbose=verbose)

      File "/net/noble/vol1/home/ranz0/bin/anaconda3/envs/py2/lib/python2.7/site-packages/segtools/signal_distribution.py", line 99, in from_segmentation

        for chromosome in chromosomes:

      File "/net/noble/vol1/home/ranz0/bin/anaconda3/envs/py2/lib/python2.7/site-packages/genomedata-1.3.6-py2.7.egg/genomedata/__init__.py", line 169, in __iter__

        yield self[groupname]

      File "/net/noble/vol1/home/ranz0/bin/anaconda3/envs/py2/lib/python2.7/site-packages/genomedata-1.3.6-py2.7.egg/genomedata/__init__.py", line 203, in __getitem__

        res = Chromosome(self.h5file, where="/" + name)

      File "/net/noble/vol1/home/ranz0/bin/anaconda3/envs/py2/lib/python2.7/site-packages/genomedata-1.3.6-py2.7.egg/genomedata/__init__.py", line 558, in __init__

        if attrs.dirty:

      File "/net/noble/vol1/home/ranz0/bin/anaconda3/envs/py2/lib/python2.7/site-packages/tables/attributeset.py", line 305, in __getattr__

        "'%s'" % (name, self._v__nodepath))

    AttributeError: Attribute 'dirty' does not exist in node: '/supercontig_0'



  5. Plot it manually by loading the genomedata to python interface (in python 3.6, I installed genomedata and did the following):
  6. >>> from genomedata import Genome

    >>> gdfilename = "/net/noble/vol3/user/karolb/results/ranz0/process2segway/test"

    >>> with Genome(gdfilename) as genome:

    ...     chromosome = genome["chr19"]

    >>> chromosome

    <Chromosome 'chr19', file='/net/noble/vol3/user/karolb/results/ranz0/process2segway/test/chr19.genomedata'>

  7. >>> data = chromosome[10000:10050, 0:3]

    Traceback (most recent call last):

      File "<stdin>", line 1, in <module>

      File "/net/noble/vol1/home/ranz0/bin/anaconda3/envs/py3.6/lib/python3.6/site-packages/genomedata/__init__.py", line 713, in __getitem__

        assert self.isopen

    AssertionError


Thanks a lot for your attention to this matter - sorry it is a lot of details, I'm been wrapping my head on it but couldn't figure out, would really appreciate your help!

Thanks,
Ran

From: ranz0 <[log in to unmask]>
Sent: Friday, July 15, 2022 4:26 PM
To: Roberts, Eric <[log in to unmask]>; segway-l: Discussion of Segway genome annotation software <[log in to unmask]>
Subject: Re: [External] Re: Rejected posting to [log in to unmask]
 
Thanks for your detailed reply, Eric! This is helpful, have a nice weekend!

Ran

From: Roberts, Eric <[log in to unmask]>
Sent: Friday, July 15, 2022 1:15 PM
To: ranz0 <[log in to unmask]>; segway-l: Discussion of Segway genome annotation software <[log in to unmask]>
Subject: Re: [External] Re: Rejected posting to [log in to unmask]
 
Each method of either vertically stacking or concatenating your data can run into their own bias issues unfortunately. Again I would refer to the SAGA review paper I linked earlier that discusses this better.

Comparing annotations across tissues is not straightforward either since it depends on what features you're trying to identify and compare. For example, you could try to identify a candidate gene list using GENCODE and your annotation by selecting what you think is a promoter-like label. You could use that list to compare GO terms, for example. But this is all very general, might not be the domain you're looking at, and is largely out the scope of the software. Segtools can help analyze your existing annotations through visualizations and analysis against reference annotations like GENCODE.
In general, I don't know a good resource off hand for general annotation comparison guidelines other than the SAGA review. Maybe someone else on the mailing list might help.

The last number is simply the "blockCount" portion of the BED file specification outlined here: https://www.genome.ucsc.edu/FAQ/FAQformat.html#format1. Practically it's only for visual formatting on the UCSC Genome Browser.

With separate annotations there's usually no 1-to-1 label comparison that can be made without some manual identification. Again, I think unfortunately the SAGA review paper is probably the best source for discussion on this. A script would probably not be general enough to work in most cases.

Hope any of that helps!

Eric




From: ranz0 <[log in to unmask]>
Sent: Thursday, July 14, 2022 4:10 AM
To: Roberts, Eric <[log in to unmask]>; segway-l: Discussion of Segway genome annotation software <[log in to unmask]>
Subject: Re: [External] Re: Rejected posting to [log in to unmask]
 
Hi Eric,

Thanks for the info! We are trying to concatenate different tissues so that we can directly compare annotations across tissues without potential bias in mapping labels across tissues, I am wondering if you have suggestions on comparing annotations across tissues?

On a related note, would it be possible to point me to some tutorial of what the last column means in segway output segway.0.bed.gz and segway.0.layered.bed.gz files? Here is the snapshot of segway.bed.gz:

chr1 3000000 85347103 0 1000 . 3000000 85347103 27,158,119 69855

chr1 3000000 85347103 1 1000 . 3000000 85347103 217,95,2 36054

chr1 3000000 85347103 10 1000 . 3000000 85347103 117,112,179 46347


Also, as I am trying to visualize and do some analysis on which region label is tissue-specific and which region is consistent across tissues (across different segway files generated for each tissue). are there some existing scripts to do that? Sorry I wasn't able to find them and would appreciate your feedback!

Thanks,
Ran

From: Roberts, Eric <[log in to unmask]>
Sent: Thursday, July 7, 2022 9:02 AM
To: ranz0 <[log in to unmask]>; segway-l: Discussion of Segway genome annotation software <[log in to unmask]>
Subject: Re: [External] Re: Rejected posting to [log in to unmask]
 
Hi,

The --reverse-world is a 0-indexed option, so if the 2nd track listed in the comma separation is the reverse stranded data, it would need to have a value of "1". There is no current way of specifying multiple worlds to reverse.

While this may seem like a significant limitation, it is often not a sought-out feature. Concatenation is the go-to way to handle stranded data but is less obviously useful or perhaps necessary with multiple cell types. For a better discussion on this you can refer to a segmentation and genome annotation review paper: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1009423. Currently the best way to handle this is to have two separate Segway models for each tissue/cell type if you wish to preserve strandedness for both. You could also vertically stack the data and concatenate across strandedness, however this depends on your use case and is discussed better in the review paper.

It is very unlikely either trained model will suffer any kind of ill fit from having the data split across cell types. On annotation comparison between tissue/cell types, you will likely have to manually map equivalent labels as best you can based on the learned parameters (using Segtools or other annotation software will likely help here).

We will discuss internally regarding whether we should attempt to engineer in a solution for future Segway releases. You can even raise the issue yourself if you wish at https://github.com/hoffmangroup/segway/issues.

Hope this helps!

Eric

From: ranz0 <[log in to unmask]>
Sent: Wednesday, July 6, 2022 9:25 PM
To: Roberts, Eric <[log in to unmask]>
Subject: Re: [External] Re: Rejected posting to [log in to unmask]
 
Hi Eric,

I'm so sorry to bother you again. I am re-reading the --reverse-world option in https://segway.hoffmanlab.org/doc/3.0.4/segway.html#segrna and doubting if I used it correctly. I have RNA-seq assays which have forward and reverse direction, as well as a bunch of other assays that are not strand-specific. I am hoping to use different assays as different tracks and concatenate Heart and Brain genomes. Would you please advise if the following track name is correct format (I duplicated non-strand-specific assays to forward and reverse strand), and what reverse-world value to specify?

Track name: "--track Heart.5mc.FFPE.forward,Heart.5mc.FFPE.reverse,Brain.5mc.FFPE.forward,Brain.5mc.FFPE.reverse --track Heart.H3K4m3.FFPE.forward,Heart.H3K4m3.FFPE.reverse,Brain.H3K4m3.FFPE.forward,Brain.H3K4m3.FFPE".

Thanks a lot for your help on this issue!
Ran


From: ranz0 <[log in to unmask]>
Sent: Wednesday, July 6, 2022 9:12 AM
To: Roberts, Eric <[log in to unmask]>
Subject: Re: [External] Re: Rejected posting to [log in to unmask]
 
Hi Eric,

Thanks a lot! These are really helpful! 

Ran

From: Roberts, Eric <[log in to unmask]>
Sent: Wednesday, July 6, 2022 7:47 AM
To: ranz0 <[log in to unmask]>
Subject: Re: [External] Re: Rejected posting to [log in to unmask]
 
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

From: ranz0 <[log in to unmask]>
Sent: Tuesday, July 5, 2022 6:19 PM
To: Roberts, Eric <[log in to unmask]>; [log in to unmask] <[log in to unmask]>
Subject: Re: [External] Re: Rejected posting to [log in to unmask]
 
Hi Eric,

Sorry to interrupt you again, I have two more questions on running segRNA:
  1. 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?
  2. 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:
  3. 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

From: Roberts, Eric <[log in to unmask]>
Sent: Monday, June 27, 2022 8:13 AM
To: ranz0 <[log in to unmask]>; [log in to unmask] <[log in to unmask]>
Subject: Re: [External] Re: Rejected posting to [log in to unmask]
 
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

From: ranz0 <[log in to unmask]>
Sent: Saturday, June 25, 2022 7:24 PM
To: Roberts, Eric <[log in to unmask]>
Subject: Re: [External] Re: Rejected posting to [log in to unmask]
 
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

From: Michael Hoffman <[log in to unmask]>
Sent: Wednesday, June 8, 2022 5:44 AM
To: ranz0 <[log in to unmask]>
Cc: Roberts, Eric <[log in to unmask]>
Subject: Re: [External] Re: Rejected posting to [log in to unmask]
 
Yes but you will probably want to duplicate the non-strand-specific data like ChIP-seq in both the forward and reverse worlds. 

On Tue., Jun. 7, 2022, 5:38 p.m. ranz0, <[log in to unmask]> wrote:
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

From: Roberts, Eric <[log in to unmask]>
Sent: Tuesday, June 7, 2022 11:31 AM
To: Michael Hoffman <[log in to unmask]>
Cc: ranz0 <[log in to unmask]>
Subject: Re: [External] Re: Rejected posting to [log in to unmask]
 

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

From: Michael Hoffman <[log in to unmask]>
Sent: Tuesday, June 7, 2022 11:08 AM
To: Roberts, Eric <[log in to unmask]>
Cc: Ran Zhang <[log in to unmask]>
Subject: [External] Re: Rejected posting to [log in to unmask]
 
[Bcc Bill]

Eric can you please help with this? M

On Mon., Jun. 6, 2022, 9:54 p.m. William Stafford Noble, <[log in to unmask]> wrote:
Thanks!  I'm cc'ing Ran, postdoc in my lab, so she knows about this.  Ran, here is the preprint:  https://www.biorxiv.org/content/10.1101/2020.07.28.225193v2

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



On Mon, Jun 6, 2022 at 4:02 PM Michael Hoffman <[log in to unmask]> wrote:
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

On Wed., Jun. 1, 2022, 11:42 p.m. William Stafford Noble, <[log in to unmask]> wrote:
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


---------- Forwarded message ---------
From: LISTSERV.UTORONTO.CA LISTSERV Server (16.0) <[log in to unmask]>
Date: Wed, Jun 1, 2022 at 8:39 PM
Subject: Rejected posting to [log in to unmask]
To: William Noble <[log in to unmask]>


You  are  not  authorized  to  send   mail  to  the  SEGWAY-L  list  from  your
[log in to unmask] account. You might be authorized to post to the list from another
account,  or perhaps  when  using  another mail  program  configured  to use  a
different email address.  However, LISTSERV has no way to  associate this other
account  or address  with yours.  If you  need assistance  or if  you have  any
questions regarding  the policy of the  SEGWAY-L list, please contact  the list
owners at [log in to unmask].



---------- Forwarded message ----------
From: William Stafford Noble <[log in to unmask]>
To: [log in to unmask]
Cc: 
Bcc: 
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


This e-mail may contain confidential and/or privileged information for the sole use of the intended recipient.
Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited.
If you have received this e-mail in error, please contact the sender and delete all copies.
Opinions, conclusions or other information contained in this e-mail may not be that of the organization.

If you feel you have received an email from UHN of a commercial nature and would like to be removed from the sender's mailing list please do one of the following:
(1) Follow any unsubscribe process the sender has included in their email
(2) Where no unsubscribe process has been included, reply to the sender and type "unsubscribe" in the subject line. If you require additional information please go to our UHN Newsletters and Mailing Lists page.
Please note that we are unable to automatically unsubscribe individuals from all UHN mailing lists.


Patient Consent for Email:

UHN patients may provide their consent to communicate with UHN about their care using email. All electronic communication carries some risk. Please visit our website here to learn about the risks of electronic communication and how to protect your privacy. You may withdraw your consent to receive emails from UHN at any time. Please contact your care provider, if you do not wish to receive emails from UHN.

This e-mail may contain confidential and/or privileged information for the sole use of the intended recipient.
Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited.
If you have received this e-mail in error, please contact the sender and delete all copies.
Opinions, conclusions or other information contained in this e-mail may not be that of the organization.

If you feel you have received an email from UHN of a commercial nature and would like to be removed from the sender's mailing list please do one of the following:
(1) Follow any unsubscribe process the sender has included in their email
(2) Where no unsubscribe process has been included, reply to the sender and type "unsubscribe" in the subject line. If you require additional information please go to our UHN Newsletters and Mailing Lists page.
Please note that we are unable to automatically unsubscribe individuals from all UHN mailing lists.


Patient Consent for Email:

UHN patients may provide their consent to communicate with UHN about their care using email. All electronic communication carries some risk. Please visit our website here to learn about the risks of electronic communication and how to protect your privacy. You may withdraw your consent to receive emails from UHN at any time. Please contact your care provider, if you do not wish to receive emails from UHN.

This e-mail may contain confidential and/or privileged information for the sole use of the intended recipient.
Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited.
If you have received this e-mail in error, please contact the sender and delete all copies.
Opinions, conclusions or other information contained in this e-mail may not be that of the organization.

If you feel you have received an email from UHN of a commercial nature and would like to be removed from the sender's mailing list please do one of the following:
(1) Follow any unsubscribe process the sender has included in their email
(2) Where no unsubscribe process has been included, reply to the sender and type "unsubscribe" in the subject line. If you require additional information please go to our UHN Newsletters and Mailing Lists page.
Please note that we are unable to automatically unsubscribe individuals from all UHN mailing lists.


Patient Consent for Email:

UHN patients may provide their consent to communicate with UHN about their care using email. All electronic communication carries some risk. Please visit our website here to learn about the risks of electronic communication and how to protect your privacy. You may withdraw your consent to receive emails from UHN at any time. Please contact your care provider, if you do not wish to receive emails from UHN.

This e-mail may contain confidential and/or privileged information for the sole use of the intended recipient.
Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited.
If you have received this e-mail in error, please contact the sender and delete all copies.
Opinions, conclusions or other information contained in this e-mail may not be that of the organization.

If you feel you have received an email from UHN of a commercial nature and would like to be removed from the sender's mailing list please do one of the following:
(1) Follow any unsubscribe process the sender has included in their email
(2) Where no unsubscribe process has been included, reply to the sender and type "unsubscribe" in the subject line. If you require additional information please go to our UHN Newsletters and Mailing Lists page.
Please note that we are unable to automatically unsubscribe individuals from all UHN mailing lists.


Patient Consent for Email:

UHN patients may provide their consent to communicate with UHN about their care using email. All electronic communication carries some risk. Please visit our website here to learn about the risks of electronic communication and how to protect your privacy. You may withdraw your consent to receive emails from UHN at any time. Please contact your care provider, if you do not wish to receive emails from UHN.

This e-mail may contain confidential and/or privileged information for the sole use of the intended recipient.
Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited.
If you have received this e-mail in error, please contact the sender and delete all copies.
Opinions, conclusions or other information contained in this e-mail may not be that of the organization.

If you feel you have received an email from UHN of a commercial nature and would like to be removed from the sender's mailing list please do one of the following:
(1) Follow any unsubscribe process the sender has included in their email
(2) Where no unsubscribe process has been included, reply to the sender and type "unsubscribe" in the subject line. If you require additional information please go to our UHN Newsletters and Mailing Lists page.
Please note that we are unable to automatically unsubscribe individuals from all UHN mailing lists.


Patient Consent for Email:

UHN patients may provide their consent to communicate with UHN about their care using email. All electronic communication carries some risk. Please visit our website here to learn about the risks of electronic communication and how to protect your privacy. You may withdraw your consent to receive emails from UHN at any time. Please contact your care provider, if you do not wish to receive emails from UHN.

This e-mail may contain confidential and/or privileged information for the sole use of the intended recipient.
Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited.
If you have received this e-mail in error, please contact the sender and delete all copies.
Opinions, conclusions or other information contained in this e-mail may not be that of the organization.

If you feel you have received an email from UHN of a commercial nature and would like to be removed from the sender's mailing list please do one of the following:
(1) Follow any unsubscribe process the sender has included in their email
(2) Where no unsubscribe process has been included, reply to the sender and type "unsubscribe" in the subject line. If you require additional information please go to our UHN Newsletters and Mailing Lists page.
Please note that we are unable to automatically unsubscribe individuals from all UHN mailing lists.


Patient Consent for Email:

UHN patients may provide their consent to communicate with UHN about their care using email. All electronic communication carries some risk. Please visit our website here to learn about the risks of electronic communication and how to protect your privacy. You may withdraw your consent to receive emails from UHN at any time. Please contact your care provider, if you do not wish to receive emails from UHN.

This e-mail may contain confidential and/or privileged information for the sole use of the intended recipient.
Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited.
If you have received this e-mail in error, please contact the sender and delete all copies.
Opinions, conclusions or other information contained in this e-mail may not be that of the organization.

If you feel you have received an email from UHN of a commercial nature and would like to be removed from the sender's mailing list please do one of the following:
(1) Follow any unsubscribe process the sender has included in their email
(2) Where no unsubscribe process has been included, reply to the sender and type "unsubscribe" in the subject line. If you require additional information please go to our UHN Newsletters and Mailing Lists page.
Please note that we are unable to automatically unsubscribe individuals from all UHN mailing lists.


Patient Consent for Email:

UHN patients may provide their consent to communicate with UHN about their care using email. All electronic communication carries some risk. Please visit our website here to learn about the risks of electronic communication and how to protect your privacy. You may withdraw your consent to receive emails from UHN at any time. Please contact your care provider, if you do not wish to receive emails from UHN.