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Old 03-25-2010, 10:51 AM   #1
BioTalk
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Default Need Graphical Viewer Tool

Hello everyone,

I would like to see the graphical view for the sequence expression with respect to the whole genome sequence. My problem is the length of graph is exceeding the normal limit of graph as I want to see the graph of whole genome sequence.

Can someone please help me if there is any tool available to see the expression value in a graphical manner.

Thank you,
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Old 03-26-2010, 01:14 AM   #2
simonandrews
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It depends on the genome :-)

SeqMonk can show a whole chromosome's worth of RNA-Seq data fairly easily in a single view as shown below:



For an organism with only one chromosome I guess that would equate to a whole genome. For multi-chromosome species you can move between chromosomes pretty quickly to get an idea of the whole genome distribution.
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Old 03-27-2010, 01:27 AM   #3
Simon Anders
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I've published a tool for this purpose last year:

S. Anders: Visualization of genomic data with the Hilbert curve.
Bioinformatics, 25 (2009), 213
http://bioinformatics.oxfordjournals...bstract/btp152

The actual software is here, but I'd recommend to look through the paper first, as the visualization technique is not full self-explaining.

Cheers
Simon
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Old 03-29-2010, 11:56 AM   #4
BioTalk
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Thank you guys for your reply. I will try using the tool you have suggested.

Thanks,
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Old 04-02-2010, 08:36 AM   #5
BioTalk
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Quote:
Originally Posted by simonandrews View Post
It depends on the genome :-)

SeqMonk can show a whole chromosome's worth of RNA-Seq data fairly easily in a single view as shown below:



For an organism with only one chromosome I guess that would equate to a whole genome. For multi-chromosome species you can move between chromosomes pretty quickly to get an idea of the whole genome distribution.
I have studied this tool and found it very user friendly and perfect for our data analysis. But my problem is, I want to see the expression of the sequences in a graphical manner. Something like the graph you have shown in your post.

So could you please tell me how can I give input of expression values and sequences and get similar graphical result.

Thanks,
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Old 04-03-2010, 01:27 AM   #6
simonandrews
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Quote:
Originally Posted by BioTalk View Post
I have studied this tool and found it very user friendly and perfect for our data analysis. But my problem is, I want to see the expression of the sequences in a graphical manner. Something like the graph you have shown in your post.

So could you please tell me how can I give input of expression values and sequences and get similar graphical result.

Thanks,
SeqMonk calculates quantitated values internally, so you just load in your mapped sequence data. You can then calculate your own expression values within the program. For RNASeq you can either calculate a value over every known existing exon, or you can build probes dynamically over contiguous clusters of reads to identify novel transcripts.

Import for RNASeq data has to come in as a SAM file (since it's the only format which supports descriptions of spliced mappings). We've tested it with TopHat output, but it should work with any other program which produces SAM files.

For the quantitation you probably want to do a base pair quantitation, corrected for probe length (to give you bp of sequence per bp of exon) - you may also want to log transform to compress your data range.

Once you've quantitated your data if you zoom out to show a whole chromosome you'll see a plot similar to the one I showed in my previous post.

If you're new to the program it probably best to have a read through the SeqMonk training course manual which provides a general introduction to how the program works, as well as having a specific section at the end on how best to apply it to RNA-Seq data.
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