[GenoMax]

Hello,

I have ace files that I would like to view and came across your MapView Software as a solution. However, I am unable to get any of the links in above messages to download a the program?

Thanks

This link is working: http://evolution.sysu.edu.cn/software/mapview.rar

Tablet also supports ace files: http://bioinf.scri.ac.uk/tablet/

[htetre]

Unable to download MapView

Hello,

I have ace files that I would like to view and came across your MapView Software as a solution. However, I am unable to get any of the links in above messages to download a the program?

Thanks

[marcovth]

Is there a known work flow from Abyss to MapView ?

[ale]

This sounds very promising! I just wonder if you are interested in natively supporting the SAM/BAM format. I think the 1000genomes project has already released some alignments in the BAM format and yet more to come in the next few months. I know it is trivial to convert SAM/BAM to MVF, but given the large amount of data (maybe >1TB data), most users would prefer viewing the alignment directly rather than duplicate them again. BAM is also compressed and indexable, and supports indels and long alignments. Sorry if this sounds like promoting projects related to myself.

Hello,

I would like to view a bam file in MapView but do not how to transform it to MVF format. Could you let me know it this can be done? That would help a lot

[demis001]

Is anyone found an answer to "System.OverflowException: Overflow error." while try to jump to the end of the chr. somewher around ~111,000,000 nc region. I have tried both 64 bit and 32 bit machine and the error appeared in both..

The detail exception spewed looks like the following. I removed few lines specific to working dir on my workstation....
==============================================================

See the end of this message for details on invoking
just-in-time (JIT) debugging instead of this dialog box.

************** Exception Text **************
System.OverflowException: Overflow error.
at System.Drawing.Graphics.CheckErrorStatus(Int32 status)
at System.Drawing.Graphics.FillRectangle(Brush brush, Single x, Single y, Single width, Single height)
at MapView.Form1.48joJTB35(Object , PaintEventArgs )
at System.Windows.Forms.Control.OnPaint(PaintEventArgs e)
at System.Windows.Forms.Control.PaintTransparentBackground(PaintEventArgs e, Rectangle rectangle, Region transparentRegion)
at System.Windows.Forms.Control.PaintBackground(PaintEventArgs e, Rectangle rectangle, Color backColor, Point scrollOffset)
at System.Windows.Forms.Control.PaintBackground(PaintEventArgs e, Rectangle rectangle)
at System.Windows.Forms.Control.OnPaintBackground(PaintEventArgs pevent)
at System.Windows.Forms.Control.PaintWithErrorHandling(PaintEventArgs e, Int16 layer, Boolean disposeEventArgs)
at System.Windows.Forms.Control.WmPaint(Message& m)
at System.Windows.Forms.Control.WndProc(Message& m)
at System.Windows.Forms.Label.WndProc(Message& m)
at System.Windows.Forms.Control.ControlNativeWindow.OnMessage(Message& m)
at System.Windows.Forms.Control.ControlNativeWindow.WndProc(Message& m)
at System.Windows.Forms.NativeWindow.Callback(IntPtr hWnd, Int32 msg, IntPtr wparam, IntPtr lparam)


************** Loaded Assemblies **************
mscorlib
Assembly Version: 2.0.0.0
Win32 Version: 2.0.50727.3603 (GDR.050727-3600)
CodeBase: file:///C:/WINDOWS/Microsoft.NET/Framework/v2.0.50727/mscorlib.dll
----------------------------------------
MapView
Assembly Version: 3.4.1.0
Win32 Version: 3.4.1.0
CodeBase: ----------------------------------------
System.Windows.Forms
Assembly Version: 2.0.0.0
Win32 Version: 2.0.50727.3053 (netfxsp.050727-3000)
----------------------------------------
System
Assembly Version: 2.0.0.0
Win32 Version: 2.0.50727.3053 (netfxsp.050727-3000)
----------------------------------------
System.Drawing
Assembly Version: 2.0.0.0
Win32 Version: 2.0.50727.3053 (netfxsp.050727-3000)
----------------------------------------
Accessibility
Assembly Version: 2.0.0.0
Win32 Version: 2.0.50727.3053 (netfxsp.050727-3000)
----------------------------------------

************** JIT Debugging **************
To enable just-in-time (JIT) debugging, the .config file for this
application or computer (machine.config) must have the
jitDebugging value set in the system.windows.forms section.
The application must also be compiled with debugging
enabled.

For example:

<configuration>
<system.windows.forms jitDebugging="true" />
</configuration>

When JIT debugging is enabled, any unhandled exception
will be sent to the JIT debugger registered on the computer
rather than be handled by this dialog box.

[yvan.wenger]

unrar problem?

Hello,
I*downloaded mapview, I*can see the files in the archive using the ubuntu 9.04 archive manager, but impossible to extract the files... Is there a password? the archive manager does like if it extracts it but the the files are not there in the end. If using the terminal, that is what I*get:

~/Desktop$ unrar -x mapview.rar

unrar 0.0.1 Copyright (C) 2004 Ben Asselstine, Jeroen Dekkers


Extracting from /home/yvan/Desktop/mapview.rar

Extracting readme.txt Failed
Extracting MVFmaker_NewFormat.txt Failed
Extracting MapView.exe Failed
3 Failed

Did anybody already experienced that and has a solution ?

Thanks a lot,
Yvan

EDIT: original source of mapview was http://evolution.sysu.edu.cn/software/mapview.rar I*however COULD*extract the zipped version there: https://sites.google.com/site/wjwdav...attredirects=0

[yina]

Hi,

Mapview is a wonderfull tool, but i was wondering, is it possible to visualize, in a single file, the frequency of each base of all the positions in the reference??

[strob]

Is this table still up to date?

http://www.sanger.ac.uk/Users/lh3/NGSalnview.shtml

[WJW-Davy]

Hello,

I would like to visualise some paired reads data using MapView. I have tried to use MVFmaker and choose the checkbox of Paired-end data. However, this checkbox is greyed out and I cannot select it.

I am using MapView version 3.4.1 under ubuntu, using mono, and it seems to work fine otherwise. Can anyone tell me how to create the MVF file for my paired reads? Thanks.

Paired reads data is only supported for SOAP format.

[lindseyjane]

MapView not working for paired reads

Hello,

I would like to visualise some paired reads data using MapView. I have tried to use MVFmaker and choose the checkbox of Paired-end data. However, this checkbox is greyed out and I cannot select it.

I am using MapView version 3.4.1 under ubuntu, using mono, and it seems to work fine otherwise. Can anyone tell me how to create the MVF file for my paired reads? Thanks.

[baohua100]

Dear baohua & Davy:

I have MAQ files converted to MVF format for visualizing, but how do I get MVR files? I used Statistics->SNP result list, but get a error message:

  <1>  2009-6-30 16:01:13 
No MVR file!

  <2>  2009-6-30 16:02:46 
No SNP results!

You should run SNP detection (on the right panel) first!

[hard998]

How to convert to MVR files?

Dear baohua & Davy:

I have MAQ files converted to MVF format for visualizing, but how do I get MVR files? I used Statistics->SNP result list, but get a error message:

  <1>  2009-6-30 16:01:13 
No MVR file!

  <2>  2009-6-30 16:02:46 
No SNP results!

[WJW-Davy]

I tried the new 3.4.1 version in Ubuntu; it analyzes coverage distribution without crashing, even on very large files!

However, in both old and new version, I noticed some problems when counting very high sequence coverage. If coverage is higher than 65536 (2^16), then the software restarts counting from one.
I attach a small table with an example. In the first column you will find the experiment number, one for each illumina tag, and in the second column you will find the coverage. I had 12 pools (one for tag), each one with a certain coverage (lower than 65536), and they summed up to a coverage of 66541. When visualizing the total sample I have for the same position a coverage of 1005, which is exactly 66541-65536.

Can you help us with this issue?
Thank you very much

MapView used only 2 bytes (16bits) to represent the number of coverage. So the max coverage was 65535. I will expand it later.

[fabio.marroni]

Coverage Issues

I tried the new 3.4.1 version in Ubuntu; it analyzes coverage distribution without crashing, even on very large files!

However, in both old and new version, I noticed some problems when counting very high sequence coverage. If coverage is higher than 65536 (2^16), then the software restarts counting from one.
I attach a small table with an example. In the first column you will find the experiment number, one for each illumina tag, and in the second column you will find the coverage. I had 12 pools (one for tag), each one with a certain coverage (lower than 65536), and they summed up to a coverage of 66541. When visualizing the total sample I have for the same position a coverage of 1005, which is exactly 66541-65536.

Can you help us with this issue?
Thank you very much

[WJW-Davy]

Mono on Ubuntu

Mono on Ubuntu:

First of all you must to install some packages. Choose "Applications->Accessories->Terminal". In the console write:

sudo apt-get install libmono-winforms2.0-cil

Write your password and software will download & install some files. Don't close the console.

Now you are able to use MapView. Just write

mono MapView.exe

The above command works only if you have saved MapView.exe file into your home directory. If you have saved the file into the desktop you must write:

mono Desktop/MapView.exe