I was hoping for some advice for bacterial Hi-C data. I have a 3D model in PDB format and was looking to convert it to .gss fomart to be used with GMOL. However the organism I'm working with only has one chromosome and no real fibres or loci. I was wondering if those files could be left empty or omitted during conversion.
Any help/advice would be greatly appreciated.
Thanks
Tash
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Our open source tool GenomeFlow that can generate a 3D model in .gss format from HiC data and visualize it is released here: https://github.com/jianlin-cheng/GenomeFlow . Please try this tool on your data. It should work well. Let us know if you have any question about how to use it.
Best,
Jianlin
Jianlin (Jack) Cheng, PhD
William and Nancy Thompson Missouri Distinguished Professor
Department of Electrical Engineering and Computer Science
MU Informatics Institute
University of Missouri - Columbia
Email: chengji@missouri.edu
Phone: 573-882-7306
Fax: 573-882-8318
Office: 109 Naka Hall
Web: http://calla.rnet.missouri.edu/cheng/
From: Anastasia Koch [tashak@users.sourceforge.net]
Sent: Wednesday, September 5, 2018 12:52 PM
To: [gmol:discussion]
Subject: [gmol:discussion] GMOL for bacterial Hi-C data
Hi
I was hoping for some advice for bacterial Hi-C data. I have a 3D model in PDB format and was looking to convert it to .gss fomart to be used with GMOL. However the organism I'm working with only has one chromosome and no real fibres or loci. I was wondering if those files could be left empty or omitted during conversion.
Based on the way, Gmol was programmed, this cannot be done because the .gss format used in Gmol is prgrammed to contain data about the lower resolution/scale such as fibre or loci at the chromosome level. Currently, we are making adjustment to the .gss format so that it can handle different formats such as the one you are trying to solve without including the lower resolution scale. The adjustment has been included in animprovement over Gmol called GenomeFlow. This work is currently under review and we are optimistic that it will be available for public use within the next few weeks. I will update my reply with the link containing the GenomeFlow software once our work is accepted. Thanks.
Tosin
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Hi
I was hoping for some advice for bacterial Hi-C data. I have a 3D model in PDB format and was looking to convert it to .gss fomart to be used with GMOL. However the organism I'm working with only has one chromosome and no real fibres or loci. I was wondering if those files could be left empty or omitted during conversion.
Any help/advice would be greatly appreciated.
Thanks
Tash
Hi Tash,
Our open source tool GenomeFlow that can generate a 3D model in .gss format from HiC data and visualize it is released here: https://github.com/jianlin-cheng/GenomeFlow . Please try this tool on your data. It should work well. Let us know if you have any question about how to use it.
Best,
Jianlin
Jianlin (Jack) Cheng, PhD
William and Nancy Thompson Missouri Distinguished Professor
Department of Electrical Engineering and Computer Science
MU Informatics Institute
University of Missouri - Columbia
Email: chengji@missouri.edu
Phone: 573-882-7306
Fax: 573-882-8318
Office: 109 Naka Hall
Web: http://calla.rnet.missouri.edu/cheng/
From: Anastasia Koch [tashak@users.sourceforge.net]
Sent: Wednesday, September 5, 2018 12:52 PM
To: [gmol:discussion]
Subject: [gmol:discussion] GMOL for bacterial Hi-C data
Hi
I was hoping for some advice for bacterial Hi-C data. I have a 3D model in PDB format and was looking to convert it to .gss fomart to be used with GMOL. However the organism I'm working with only has one chromosome and no real fibres or loci. I was wondering if those files could be left empty or omitted during conversion.
Any help/advice would be greatly appreciated.
Thanks
Tash
GMOL for bacterial Hi-C datahttps://sourceforge.net/p/gmol/discussion/general/thread/3610150a/?limit=25#cec8
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Hi Tash,
Based on the way, Gmol was programmed, this cannot be done because the .gss format used in Gmol is prgrammed to contain data about the lower resolution/scale such as fibre or loci at the chromosome level. Currently, we are making adjustment to the .gss format so that it can handle different formats such as the one you are trying to solve without including the lower resolution scale. The adjustment has been included in animprovement over Gmol called GenomeFlow. This work is currently under review and we are optimistic that it will be available for public use within the next few weeks. I will update my reply with the link containing the GenomeFlow software once our work is accepted. Thanks.
Tosin