[baohua100]

MapView 3.1.2 is released!

If you have some suggestions or bugs, please post here! Thanks!

[bioinfosm]

Thanks baohua.
Whats the changelog? Is there a command-line version using x-windows maybe?

[garwuf]

indels

First, I would like to thank you guys for this useful tool. I have tried it on several datasets and found its performance to be more than adequate. I have one question: I have noticed that the viewer handles the alignments as ungapped even if I feed it with gapped ones (like soap1 or seqmap outputs). Actually, the very nature of input information for the viewer suggests that it positions only the first base of a read against reference sequence, but not every base. So, I wonder if you have any plans to make Mapview to visualize indels?

[baohua100]

Thanks! bioinform! Sorry, there is not a command-line version using x-windows now.

Thanks baohua.
Whats the changelog? Is there a command-line version using x-windows maybe?

[baohua100]

Thanks for your reply! MapView 3.1.2 only support for visualization of ungapped alignment. We will add the function of gapped and spliced alignment later.

First, I would like to thank you guys for this useful tool. I have tried it on several datasets and found its performance to be more than adequate. I have one question: I have noticed that the viewer handles the alignments as ungapped even if I feed it with gapped ones (like soap1 or seqmap outputs). Actually, the very nature of input information for the viewer suggests that it positions only the first base of a read against reference sequence, but not every base. So, I wonder if you have any plans to make Mapview to visualize indels?

[lparsons]

I tried to run MapView using Mono on a Mac OS X 10.5. It started, displayed the window briefly, the crashed with this error:

System.NotImplementedException: The requested feature is not implemented.
at System.Windows.Forms.XplatUICarbon.get_CursorSize () [0x00000]
at System.Windows.Forms.XplatUI.get_CursorSize () [0x00000]
at System.Windows.Forms.SystemInformation.get_CursorSize () [0x00000]
at MapView.Form1.abmmeKAlo (System.Object , System.EventArgs ) [0x00000]
at System.Windows.Forms.Form.OnLoad (System.EventArgs e) [0x00000]
at System.Windows.Forms.Form.OnLoadInternal (System.EventArgs e) [0x00000]
Segmentation fault

Any suggestions? Thanks.

[lparsons]

I ran the software on Windows, and was able to get it running. However, after converting a MAQ alignment to MVF, when I load the MVF file, I get an error:

Arithmetic operation resulted in an overflow.

[baohua100]

The paper is published on Bioinformaitcs.

MapView: visualization of short reads alignment on a desktop computer

http://bioinformatics.oxfordjournals...bstract/btp255

[bioinfosm]

congrats baohua!
It would be great if you could keep a running log of changes for newer versions

[nilshomer]

. 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.

I have to reiterate the point lh3 is making. SAM/BAM format would be great if you could support it, since even people outside of 1000 genomes have generated 100's of GBs of data in SAM/BAM. Also, paired end info, indels, quality scores, complex references, and the ability to add arbitrary annotation and post-alignment "tracks" (maybe interact with a backend database?) would be the killer application.

[strob]

Hello,

I'm using Mapview and it works fine. A feature that could be useful to be included is to show the reference and its coverage. Not on top like now, but maybe as a separate feature, having the reference presented as a bar and the parts which are covered could have a certain color (maybe depending on the amount of reads covering that region). In this way I could compare my annotation shown in a GenomeBrowser with the mapping of my exon reads on the reference.

Many thanks

[WJW-Davy]

The new version is being planned. We are discussing the new features.
SAM/BAM format will be supported.
A command line version will be available.
... ...

[Drake]

Hello,
is there a way to export the SNP list to a flat file? Like the one maq produces?

Thanks!

[WJW-Davy]

Hello,
is there a way to export the SNP list to a flat file? Like the one maq produces?

Thanks!

3.1.4 [2009.5.2]

Text can be copyed from SNP list.
MVR file can be converted to text file. The SNP list can be exported to a flat file.

[garwuf]

to Drake

<i>is there a way to export the SNP list to a flat file? Like the one maq produces?</i>

I'm using HyperSnap (screen capture program) for that. It has text capture mode, can get text from scrolling windows and output it in tab-delimited format. I guess SnagIt also might do something like that. Unfortunately, both these software pieces are commercial.