Tracks on Genome Browser

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Tracks on Genome Browser

Claudia Armenise
Dear Madam, Dear Sir,

I'm a French bioinformatician working on deep-sequencing of small RNA. I
would like to visualize my data on your Genome Browser tool... I have a
file *.bed and I can visualize my data (I made a screenshot "what I
have.png") and I would like to know if it's possible to visualize them
differently (I made a screenshot from another dataset "what I
want.png").

Is it possible ? Do I need to upload another type of file ?

Thank you for your answer

Best regards,

Claudia ARMENISE

--
 Mlle Claudia ARMENISE
Bioinformatics Enginneer
Institut de Génétique Humaine/CNRS Montpellier
E-mail : [hidden email]


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Re: Tracks on Genome Browser

Lincoln Stein
Hi Claudia,

This should be possible if the genome browser in question is running the very latest version of the software. After uploading, you ought to be able to go to the little tool icon on the titlebar, and enter "1000" in the text box that says "Show summary when region >=". This will activate a histogram whenever the view is greater than 1000 bp, which is the practical limit for such a view. However, this will only work if the admins are running the newest version.

Otherwise, you can achieve the effect you want by converting your data into a wiggle-format file (see the UCSC genome browser's documentation on WIG) and uploading that. What you'll need to do is to sort all the features from left to right, then take a 1 kb (or smaller) window that moves from left to right, and count up the number of features that overlaps each window in order to generate a file that maps interval to coverage. There ought to be an online tool to do that (e.g. in Galaxy) but I couldn't find one after a brief search.

Which genome browser instance are you uploading your data to?

Lincoln

On Wed, Jun 30, 2010 at 12:26 PM, Claudia Armenise <[hidden email]> wrote:
Dear Madam, Dear Sir,

I'm a French bioinformatician working on deep-sequencing of small RNA. I
would like to visualize my data on your Genome Browser tool... I have a
file *.bed and I can visualize my data (I made a screenshot "what I
have.png") and I would like to know if it's possible to visualize them
differently (I made a screenshot from another dataset "what I
want.png").

Is it possible ? Do I need to upload another type of file ?

Thank you for your answer

Best regards,

Claudia ARMENISE

--
 Mlle Claudia ARMENISE
Bioinformatics Enginneer
Institut de Génétique Humaine/CNRS Montpellier
E-mail : [hidden email]


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--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>

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Screenshot-C. elegans genes: 40 kbsummary_mode.png (41K) Download Attachment