RSEG Users

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The RSEG software package is aimed to analyze ChIP-Seq data, especially for identifying genomic regions and their boundaries marked by diffusive histone modification markers, such as H3K36me3 and H3K27me3. It can work with or without control sample. It can be used to find regions with differential histone modifications patterns, either comparsion between two cell types or between two kinds of histone modifications.

Homepage: http://smithlab.usc.edu/histone/rseg/

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cc1...@essex.ac.uk

7/15/17

rseg segmentation fault core dumped

I am interested in using your package- 'rseg' for differential peak calling between treated

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rseg segmentation fault core dumped

I am interested in using your package- 'rseg' for differential peak calling between treated

7/15/17

akeyar...@gmail.com

5/23/17

About RSEG simulated H3K36me3 test dataset

Hi all I'm trying to use the H3K36me3 simulated data(lib-k36-6000a.bed) but domain information of

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About RSEG simulated H3K36me3 test dataset

Hi all I'm trying to use the H3K36me3 simulated data(lib-k36-6000a.bed) but domain information of

5/23/17

Alex Koeppel, … Andrew D. Smith10

8/19/16

estimated run time for deadzones

You read it correctly. But if you start using more memory than the physical memory available on your

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estimated run time for deadzones

You read it correctly. But if you start using more memory than the physical memory available on your

8/19/16

Haitham Ashoor, Song, Qiang2

1/28/16

RSEG issue

Hi Haitham, Sorry for the late reply. That error message usually indicates that there is no

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RSEG issue

Hi Haitham, Sorry for the late reply. That error message usually indicates that there is no

1/28/16

Michael Seidl, Song, Qiang7

1/4/16

Domain for CenH3 peak

Hi, thanks a lot for your reply. Good to know that there is an 'easy' fix...Strange indeed :)

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Domain for CenH3 peak

Hi, thanks a lot for your reply. Good to know that there is an 'easy' fix...Strange indeed :)

1/4/16

rspreafico, Song, Qiang2

10/11/15

Mixed-length reads

Hi Roberto, Your understanding is right. If the reads have variable length, the deadzone correction

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Mixed-length reads

Hi Roberto, Your understanding is right. If the reads have variable length, the deadzone correction

10/11/15

MIRIAM GAGLIARDI

6/30/15

rseg-diff: ../common/TwoStateScaleSplitResolveMixture.cpp:57: Assertion `val_weight > 0' failed

Hi, I ran RSEG with the following script: #!/bin/bash #PBS -o /home/userA/RSEG_protein1/RSEG_MG_30-6-

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rseg-diff: ../common/TwoStateScaleSplitResolveMixture.cpp:57: Assertion `val_weight > 0' failed

Hi, I ran RSEG with the following script: #!/bin/bash #PBS -o /home/userA/RSEG_protein1/RSEG_MG_30-6-

6/30/15

Toby Hocking, Song, Qiang4

8/18/14

Varying the number of enriched domains detected

Hi Toby, You may try to tune the -posterior-cutoff parameter. This parameter indicates the posterior

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Varying the number of enriched domains detected

Hi Toby, You may try to tune the -posterior-cutoff parameter. This parameter indicates the posterior

8/18/14

Abdulrahman Salhab, Song, Qiang3

8/4/14

different result between rseg(0.4.4) and rseg(0.4.8RC)

Hi Song, thanks for your reply. I will do what you suggested best Abdulrahman On Friday, August 1,

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different result between rseg(0.4.4) and rseg(0.4.8RC)

Hi Song, thanks for your reply. I will do what you suggested best Abdulrahman On Friday, August 1,

8/4/14

Toby Hocking, Song, Qiang3

7/31/14

"reads not sorted" in a sorted bam file

Thanks for the helpful reply. I eventually got rseg-diff to work by first converting the bam files to

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"reads not sorted" in a sorted bam file

Thanks for the helpful reply. I eventually got rseg-diff to work by first converting the bam files to

7/31/14

memphismadison, Song, Qiang2

5/30/14

downstream analysis

Hi Rod, The output file from RSEG follows the BED file format in UCSC Genome Browser. We have some in

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downstream analysis

Hi Rod, The output file from RSEG follows the BED file format in UCSC Genome Browser. We have some in

5/30/14

Ximena Bonilla, Song, Qiang3

11/6/13

Rseg output folders/files

Oh, thank you! that was the problem Ximena On Tuesday, November 5, 2013 2:14:32 AM UTC+1, Qiang Song

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Rseg output folders/files

Oh, thank you! that was the problem Ximena On Tuesday, November 5, 2013 2:14:32 AM UTC+1, Qiang Song

11/6/13

julie, Song, Qiang3

9/6/13

ERROR: reads not sorted while the reads are sorted

Thanks a lot! It works. Julie On Tuesday, September 3, 2013 10:13:34 AM UTC+2, julie wrote: Hi, I

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ERROR: reads not sorted while the reads are sorted

Thanks a lot! It works. Julie On Tuesday, September 3, 2013 10:13:34 AM UTC+2, julie wrote: Hi, I

9/6/13

julie, … Song, Qiang3

6/10/13

Error with rseg diff : "gsl/gamma.c ERROR" or "Assertion val_weight>0 failed"

Hi Shen, I have not figure out the exact cause of this issue since I don't have a test dataset to

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Error with rseg diff : "gsl/gamma.c ERROR" or "Assertion val_weight>0 failed"

Hi Shen, I have not figure out the exact cause of this issue since I don't have a test dataset to

6/10/13

julie, Song, Qiang4

1/2/13

Help for option usage

Our galaxy website with rseg is not publicly available at this time. On Wed, Jan 2, 2013 at 4:25 AM,

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Help for option usage

Our galaxy website with rseg is not publicly available at this time. On Wed, Jan 2, 2013 at 4:25 AM,

1/2/13

julie, Song, Qiang7

12/12/12

memory allocation error in one pc and no in another!

Sorry, it's an error! Effectively I try to run this new version with old options. With the new

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memory allocation error in one pc and no in another!

Sorry, it's an error! Effectively I try to run this new version with old options. With the new

12/12/12

Bob

8/16/12

join program

Hello all, I need to make deadzone coordinates for 25-base reads mm9 library. So far, I managed to

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join program

Hello all, I need to make deadzone coordinates for 25-base reads mm9 library. So far, I managed to

8/16/12

Andreas Gschwind

4/17/12

Significant boundaries and read density

Hi, I am using rseg to call various histone modifications such as h3k27me3, h3k4me3 and h3k4me1. When

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Significant boundaries and read density

Hi, I am using rseg to call various histone modifications such as h3k27me3, h3k4me3 and h3k4me1. When

4/17/12

Kadir Akdemir, Song, Qiang3

4/16/12

What's the average run time of Rseg

Hi Song, Thanks for your prompt reply. I changed used the training parameter as you suggested. It

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What's the average run time of Rseg

Hi Song, Thanks for your prompt reply. I changed used the training parameter as you suggested. It

4/16/12

Dario Beraldi, Song, Qiang3

4/12/12

Option -domain-size

Once again, thanks for explanation. Dario On Apr 12, 5:43 am, "Song, Qiang" <qiang.s...@

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Option -domain-size

Once again, thanks for explanation. Dario On Apr 12, 5:43 am, "Song, Qiang" <qiang.s...@

4/12/12

dario, … Song, Qiang6

3/22/12

Downsampling chip / control

Hi Robert, You are right that library size affects the parameter estimation, but it affects both the

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Downsampling chip / control

Hi Robert, You are right that library size affects the parameter estimation, but it affects both the

3/22/12

Andreas Gschwind, Song, Qiang3

2/23/12

running rseg WITH duplicated reads

Cool, thanks! On Feb 23, 7:14 am, "Song, Qiang" <qiang.s...@usc.edu> wrote: > Hi

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running rseg WITH duplicated reads

Cool, thanks! On Feb 23, 7:14 am, "Song, Qiang" <qiang.s...@usc.edu> wrote: > Hi

2/23/12

dario, Song, Qiang3

2/22/12

Filtering multi-mapping reads

Ok, got it. Many thanks for your reply. (I might come back with more questions in a separate thread..

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Filtering multi-mapping reads

Ok, got it. Many thanks for your reply. (I might come back with more questions in a separate thread..

2/22/12

dawe, … Song, Qiang4

2/16/12

Score usage

On Wed, Feb 15, 2012 at 1:08 AM, Davide Cittaro <daweo...@gmail.com> wrote: On Feb 15, 2012,

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Score usage

On Wed, Feb 15, 2012 at 1:08 AM, Davide Cittaro <daweo...@gmail.com> wrote: On Feb 15, 2012,

2/16/12

M.Sammeth, … micha3

9/1/11

Fwd: RMAPOptionException

Sure, thanks. micha On Aug 31, 8:23 pm, "Song, Qiang" <qiang.s...@usc.edu> wrote:

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Fwd: RMAPOptionException

Sure, thanks. micha On Aug 31, 8:23 pm, "Song, Qiang" <qiang.s...@usc.edu> wrote:

9/1/11

Li-Wei, Song, Qiang2

8/30/11

rseg-diff running error

Hi Li-Wei, It seems that RSEG ran into some strange estimates of the domain sizes. Could you please

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rseg-diff running error

Hi Li-Wei, It seems that RSEG ran into some strange estimates of the domain sizes. Could you please

8/30/11

Li-Wei, Song, Qiang2

8/25/11

memory allocation error running deadzones

Hi Li-Wei, First of all, using deadzone correction significantly improves the performance of RSEG. It

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memory allocation error running deadzones

Hi Li-Wei, First of all, using deadzone correction significantly improves the performance of RSEG. It

8/25/11

dawe, Song, Qiang5

7/13/11

Error in running rseg (val_weight >0 assertion failed)

On Jul 13, 2011, at 6:12 AM, Song, Qiang wrote: Hi Davide, Thanks for bringing this problem to our

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Error in running rseg (val_weight >0 assertion failed)

On Jul 13, 2011, at 6:12 AM, Song, Qiang wrote: Hi Davide, Thanks for bringing this problem to our

7/13/11

Matthew Peterson, Song, Qiang2

6/21/11

Compiling RSEG on Mac

Hi Matthew, I am sorry, but we do not have plan to support Mac OS right now. If you really needs to

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Compiling RSEG on Mac

Hi Matthew, I am sorry, but we do not have plan to support Mac OS right now. If you really needs to

6/21/11

Kristina, Song, Qiang7

6/21/11

Assertion `check_sorted(raw_regions, false)' failed.

Hi Kristina, It seems the binning reads function does not work as expected in your cae. But It is

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Assertion `check_sorted(raw_regions, false)' failed.

Hi Kristina, It seems the binning reads function does not work as expected in your cae. But It is

6/21/11