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Old 03-22-2012, 09:07 AM   #1
sbrohee
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Default visualisation of chip-seq profiles ... seqminer?

Dear chip-seq experts ,

My boss would like to have fancy chip-seq profiles (reads arounds TSS) for ... yesterday!
I am quite new to the chip-seq world and I was already very happy to have extracted peaks from his data.

Would you know a tool that allows an easy peak visualization starting from the bowtie alignement files? I read that seqminer was able to perform this kind of task but was unable to use it.

After having loaded my bowtie file, I get an error : "you haven't chosen a peak reference" and I am quite lost!

I don't absolutely want to use seqminer and I'm not reluctant to use R or another tool that could be more appropriate.

So, if you get an idea, please, give me a hint. To my opinion, it should not be that difficult, isn't it?

Thank you all for your help,

Sylvain
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Old 04-13-2012, 05:47 AM   #2
artsinyc
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Hi Sylvain,
You may want to try our tool for peak profiles and heatmaps:
http://code.google.com/p/ibm-cbc-genomic-tools/
The issue with this kind of visual representations is that every case seems to be different, because everybody wants slight variations of the same thing :-) Anyway, try out our tool if you like (make sure you download the latest version), and let me know if you have questions!
Ari
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Old 04-16-2012, 05:48 AM   #3
sbrohee
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Hi Ari,

Thanks for your proposition, I'll try your tool!

However, as I did not get any answer in the beginning, I decided to implement my own tool myself (very simple, in fact). I don't know if I'll make it available publicly cause the code is pretty ugly (mix of R and Perl) but the idea is to give a GTF and a WIG file as input, to specify a gene, and it produces the kind of output in attachment.

Of course, if my tool interests someone, I'll be more than happy to share the (awful code)

Cheers,

Sylvain
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File Type: pdf gata4.pdf (27.9 KB, 117 views)
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Old 05-02-2012, 07:00 AM   #4
sbrohee
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Dear all,

I just finished the web implementation of my small visualization tool for binding profiles.

Interested users can test it on http://rsat.ulb.ac.be/~sylvain/binding_profiles/binding_profiles_form.php]this adress

Any feedback is welcome, of course!

Sylvain

Last edited by sbrohee; 10-30-2012 at 05:55 AM.
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Old 10-30-2012, 05:57 AM   #5
sbrohee
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Dear all,

My tool, called D-peaks, has just been published in Transcription. I think I can now close the subject.

La boucle est bouclée.
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