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Old 04-21-2009, 01:12 AM   #41
strob
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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
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Old 04-27-2009, 06:09 PM   #42
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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.
... ...
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Old 04-28-2009, 12:47 PM   #43
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Hello,
is there a way to export the SNP list to a flat file? Like the one maq produces?

Thanks!
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Old 04-28-2009, 05:46 PM   #44
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Originally Posted by Drake View Post
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.
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Old 05-01-2009, 09:36 AM   #45
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<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.
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Old 05-01-2009, 10:22 AM   #46
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Thanks for your answers ..

It's a pity that there is no simple button to export this region ... so I will stay with my MAQ flat files in cyqwin ...
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Old 05-01-2009, 07:40 PM   #47
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Default MapView 3.1.4 The SNP list can be exported to a flat file.

Download Link : https://sites.google.com/site/wjwdavy/

[Change Log - main versions]

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.


3.0 [2009.3.8]
Significant improvement.
Quality Score, Paired-end data, structure variation, coverage distribution, quality distribution, text quick view, zoom in/out, and other features are supported.

2.0 [2008.12.16]
Significant improvement.
Support many formats. Fasta format and text-based alignment results file(output by Eland, Maq, SOAP, MapNext, SeqMap … …).

1.0 [2008.11.28]
This is the first attempt.
Only support MapNext's format
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Old 05-01-2009, 07:45 PM   #48
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Originally Posted by garwuf View Post
<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.
Quote:
Originally Posted by Drake View Post
Thanks for your answers ..

It's a pity that there is no simple button to export this region ... so I will stay with my MAQ flat files in cyqwin ...
MapView 3.1.4 can export the SNP list to a flat file. You can text from SNP list.
It has the simple button now. ^_^
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Old 05-01-2009, 07:51 PM   #49
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That's awesome! ... You added this feature very quick! Thanks a lot! I really appreciate!
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Old 05-01-2009, 08:02 PM   #50
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There is another question I have and you might think about?
I am doing a lot of comparisons and therefore I am jumping between two views a lot.
So for my analysis it would be useful to load e.g. two different MVR files into the program with a split screen and to scroll through both screens at the same time.
I don't know how complicated it could be to add or even how useful it could be for other people, but maybe this is something you would be interested in?

Thanks!
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Old 05-02-2009, 02:05 AM   #51
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Quote:
Originally Posted by Drake View Post
There is another question I have and you might think about?
I am doing a lot of comparisons and therefore I am jumping between two views a lot.
So for my analysis it would be useful to load e.g. two different MVR files into the program with a split screen and to scroll through both screens at the same time.
I don't know how complicated it could be to add or even how useful it could be for other people, but maybe this is something you would be interested in?

Thanks!
like that?


At present, you can run many MapViews and load many MVF files.
In one MapView, you can open many SNP Lists.
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Old 05-02-2009, 04:27 AM   #52
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Yes .. that's the way I do it now.

But I am looking for something to do it simultaneously. I have attached a screenshot where I have put two views horizontal. Now it would be nice, to have these two screens position-wise exactly one above the other. And one scroll bar between them to scroll at the same time through both alignments.
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Old 05-05-2009, 04:33 AM   #53
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Originally Posted by strob View Post
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
Great! I have started a new version and will add this feature.
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Old 05-05-2009, 08:56 AM   #54
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Quote:
Originally Posted by strob View Post
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
What would be useful would be a feature to export the coverage in a BED/WIGgle file that could be ready by GenomeBrowser or other similar tools. It would eliminate an extra step in my processing pipeline.

Of course, the killer feature would to be able to visualize the various annotation tracks on GenomeBroswer from within MapView along with the reads. I've seen a few commercial programs that do this, but even they were still a bit clunky.
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Old 05-06-2009, 07:36 AM   #55
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Hi again,
I became really interested in MapView; but unfortunately there are a few things making the output hard to trust.
For example: I have a bad reference strain (bad means that there are ambiguous bases 'N' or 'S' in it). Then MapView produces an odd output for the reference. I have attached two cut screen shots. One is from MapView and one is from the NCBI viewer. Both have the same reference sequence.
When you look at the MapView output, you see that on position 71275 and 71277 are ambiguous bases. Now look on the position after these two (71276, 71278 and 71279) .. you will see three 'T's and only one of the is true. You can easily compare it with the NCBI view. The marker is positioned on 71275. Position 71276 is a 'G', 71278 is a 'T' (this one is correct) and 71279 is a 'C'.

Any suggestions why this happens?
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File Type: jpg ncbiView.JPG (17.7 KB, 13 views)

Last edited by Drake; 05-06-2009 at 07:38 AM.
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Old 05-06-2009, 07:55 AM   #56
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Quote:
Originally Posted by Drake View Post
Hi again,
I became really interested in MapView; but unfortunately there are a few things making the output hard to trust.
For example: I have a bad reference strain (bad means that there are ambiguous bases 'N' or 'S' in it). Then MapView produces an odd output for the reference. I have attached two cut screen shots. One is from MapView and one is from the NCBI viewer. Both have the same reference sequence.
When you look at the MapView output, you see that on position 71275 and 71277 are ambiguous bases. Now look on the position after these two (71276, 71278 and 71279) .. you will see three 'T's and only one of the is true. You can easily compare it with the NCBI view. The marker is positioned on 71275. Position 71276 is a 'G', 71278 is a 'T' (this one is correct) and 71279 is a 'C'.

Any suggestions why this happens?

This a little bug about ambiguous base. We will fix it soon!

Thank you for your message!
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Old 05-06-2009, 08:12 PM   #57
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Quote:
Originally Posted by Drake View Post
Hi again,
I became really interested in MapView; but unfortunately there are a few things making the output hard to trust.
For example: I have a bad reference strain (bad means that there are ambiguous bases 'N' or 'S' in it). Then MapView produces an odd output for the reference. I have attached two cut screen shots. One is from MapView and one is from the NCBI viewer. Both have the same reference sequence.
When you look at the MapView output, you see that on position 71275 and 71277 are ambiguous bases. Now look on the position after these two (71276, 71278 and 71279) .. you will see three 'T's and only one of the is true. You can easily compare it with the NCBI view. The marker is positioned on 71275. Position 71276 is a 'G', 71278 is a 'T' (this one is correct) and 71279 is a 'C'.

Any suggestions why this happens?
It is about dealing with ambiguous bases. I have found the bug and fixed it. Thank you.

I will release the new version as soon as possible. And sta2txt feature will be added.
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Old 05-07-2009, 02:02 AM   #58
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download link:https://sites.google.com/site/wjwdav...attredirects=0

3.2.0 [2009.5.7]
The bug about dealing with ambiguous nucleotides was fixed. (Note: In order to deal with ambiguous nucleotides correctly, new MVF file should be made. )
sta2txt feature was added.
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Old 05-10-2009, 01:17 AM   #59
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3.3.0 [2009.5.10]
The feature 'Overview Bar' map was added.
Double-click one line of SNP list to jump to its position not its SNP No.

Download Link 1: https://sites.google.com/site/wjwdav...attredirects=0

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Old 05-18-2009, 12:05 PM   #60
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Default variant frequency

Hello again,
Can anyone explain me how the 'VariantFrequency' in the stat file is calculated?
I mean, it's obvious how the frequency is calculated for one variant base. But how is it done for two or three variant bases?
I also attached an excerpt from my stat file. Row 369 and 370 are clear to me, but would anyone be so kind to explain me the other two?

Thanks in advance!
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