[zlu]

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to get hold of a copy of MagicViewer but the download link at the site (http://bioinformatics.zj.cn/magicviewer/) is no longer valid.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?

[Michael.James.Clark]

Always good to see more options out there for viewers.

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!

[biofqzhao]

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.

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

[Yilong Li]

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

[biofqzhao]

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

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

[Yilong Li]

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

[niraj]

hello friends,

Help me solve the problem with Magic Viewer

I have .fa file as reference sequence. I aligned the illumina mate pair reads using to the ref. seq using soapaligner and converted the mapped file to .sam format. But when I am using these files in magic viewer, the reads are not seen in the window...Can someone tell me the right steps for this..

Regards,
Niraj

[houhuabin]

Hello,
Our MagicViewer has been informed to be published in Nucleic Acids Research. This software is mainly for contributions to various genome studies, including de novo sequencing, transcriptome sequencing and targeted re-sequencing. Users are freely accessed to short reads alignment visualization, genetic variation detection and annotation in an intuitive way. We appreciate so much concern, support and feedbacks to us.

We are expecting any comment, suggestions or questions for later MagicViewer update.

Best regards,

Huabin Hou

[houhuabin]

New latest MagicViewer Version 1.1.6 has been released, which can display SNPs heterozygosis and homozygosis along with several bugs fixed.

Welcome any comment and suggestion to help to enhance its power and ofuture update.

[houhuabin]

Hi byb121,

This is not a real bug, it is caused by the quality type of your file. Are your date in Sanger format? Perhapse you can try Settings->Project Parameters-> Quality Type->Sanger.

[byb121]

Hi,

I am using Ubuntu 910 64-bit.

I tried the new magicviewer 1.1.5 64 bit linux version, it stuck in in somewhere else this time.

This is what shows in the terminal.

$ sh MagicViewer.sh
/home/transcriptsData/GSE11209/ana/magicviewer/SRX000559.SRR002051.map.sorted.bam.bai---------bamIndexFile-------

"index reference file" window will not close automatically(shown in attachment screen1).

After I closed the window, I found no stack view of reads, but when mouse pointer moved onto any position where a read is supposed to be, I still get information about the reads ( shown in screen2).

[houhuabin]

Hi,

The new version of MagicViewer(Ver. 1.1.5 ) have released now.
The bugs reported by zhao and byb121 have fixed. You can try it now, If you have any questions, please don't hesitate to contact us.

Thanks

Huabin

[houhuabin]

Dear byb121,

Thanks for using MagicViewer!
Could you tell me whether your computer is linux 32 or 64 bit?

Huabin

[byb121]

Dear huabin,

I just tried magicviewer, I would say it's an easy to use software with beautiful interface, nice work!
It runs smoothly in windows, but there is a flaw (probably my fault as I am a new linux user) in Linux, the same files that worked fine in windows couldn't be loaded in my Ubuntu system.

$sudo sh MagicViewer.sh
java.io.FileNotFoundException: /transcriptsData/GSE11209/ana/magicviewer/SRX000559.SRR002051.map.sorted.bam.bai (No such file or directory)
	at java.io.FileInputStream.open(Native Method)
	at java.io.FileInputStream.<init>(FileInputStream.java:106)
	at java.io.FileInputStream.<init>(FileInputStream.java:66)
	at utils.Remove0D.remove(Remove0D.java:28)
	at utils.SamViewUtil.rm0d(SamViewUtil.java:116)
	at utils.SamViewUtil.processAlignmentFile(SamViewUtil.java:102)
	at Magic.WinMain.NewBAMJDialog$8.construct(NewBAMJDialog.java:351)
	at Magic.Units.Gui.SwingWorker$2.run(SwingWorker.java:115)
	at java.lang.Thread.run(Thread.java:619)
Exception in thread "Thread-9" net.sf.picard.PicardException: Unable to load fasta index file /transcriptsData/GSE11209/ana/magicviewer/sacCer.fa.fai.  Please create it using 'samtools faidx'.
	at org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile.loadIndex(IndexedFastaSequenceFile.java:121)
	at org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile.<init>(IndexedFastaSequenceFile.java:60)
	at Magic.Units.Main.ViewerLog.setViewerLog(ViewerLog.java:52)
	at Magic.WinMain.NewBAMJDialog$8.construct(NewBAMJDialog.java:354)
	at Magic.Units.Gui.SwingWorker$2.run(SwingWorker.java:115)
	at java.lang.Thread.run(Thread.java:619)

My java is fine (at least I believe so).

$ java -version
java version "1.6.0_15"
Java(TM) SE Runtime Environment (build 1.6.0_15-b03)
Java HotSpot(TM) 64-Bit Server VM (build 14.1-b02, mixed mode)

Any suggestion to get around with it?
Thanks

[houhuabin]

Dear zhao,

Sorry for inform you so late.
The MagicViewer can now surport suffix of "fna" and "faa" in the lastest version, and we have solved the bugs of index fasta file in mac, after regression testing we will release in the next version.

Thanks!