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Old 02-10-2011, 12:43 AM   #21
Yilong Li
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Location: WTSI

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Hi,

I want to visualize some next generation sequencing data for human (big reference contigs and a lot of sequences) and try to look at paired reads located at putative genomic rearrangements. MagicViewer seems interesting! I am wondering whether MagicViewer is able to illustrate paired reads properly (by i.e. linking them).

Yilong
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Old 02-10-2011, 12:59 AM   #22
biofqzhao
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Location: Penn State

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We have another tool (ingap-sv) to visualize paired reads. Please refer to http://ingap.sourceforge.net/
We are still testing this software. An updated version will be uploaded very soon.

Fangqing

Quote:
Originally Posted by Yilong Li View Post
Hi,

I want to visualize some next generation sequencing data for human (big reference contigs and a lot of sequences) and try to look at paired reads located at putative genomic rearrangements. MagicViewer seems interesting! I am wondering whether MagicViewer is able to illustrate paired reads properly (by i.e. linking them).

Yilong
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Old 02-11-2011, 11:07 AM   #23
Yilong Li
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Hi Fangqing,

Thanks for the tip! I downloaded your program and it seems quite interesting. I wonder if your program will be able to handle genomic sequencing data and reference .fasta files from human genome, at a regular desktop. I noticed that your program does not require pre-indexed fastas or bams.

I could not test it yet today, since the program was unable to read in .sam files with @-headers, but complained that I didn't have proper .sam files. So for your upcoming version, this could be a rather useful and easy fix .

I am now creating a new .sam file with @-header stripped, and looking forward to see the results!

Yilong
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Old 02-11-2011, 07:07 PM   #24
biofqzhao
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Could you please let me know how did you generate this sam file? If possible, please send me your sam file (or its first 1000 lines). I will test it by myself. Thanks.

Quote:
Originally Posted by Yilong Li View Post
Hi Fangqing,

Thanks for the tip! I downloaded your program and it seems quite interesting. I wonder if your program will be able to handle genomic sequencing data and reference .fasta files from human genome, at a regular desktop. I noticed that your program does not require pre-indexed fastas or bams.

I could not test it yet today, since the program was unable to read in .sam files with @-headers, but complained that I didn't have proper .sam files. So for your upcoming version, this could be a rather useful and easy fix .

I am now creating a new .sam file with @-header stripped, and looking forward to see the results!

Yilong
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Old 02-11-2011, 07:41 PM   #25
Michael.James.Clark
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Location: Palo Alto

Join Date: Apr 2009
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Always good to see more options out there for viewers.

Quote:
Originally Posted by Yilong Li View Post
Hi,

I want to visualize some next generation sequencing data for human (big reference contigs and a lot of sequences) and try to look at paired reads located at putative genomic rearrangements. MagicViewer seems interesting! I am wondering whether MagicViewer is able to illustrate paired reads properly (by i.e. linking them).

Yilong
IGV can do this. You may want to try it out!
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Old 02-20-2012, 07:06 AM   #26
zlu
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Hi,

I'm trying to get hold of a copy of MagicViewer but the download link at the site (http://bioinformatics.zj.cn/magicviewer/) is no longer valid. Is the program still available?

Last edited by zlu; 02-20-2012 at 07:46 AM.
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