visualisation of chip-seq profiles ... seqminer?

sbrohee · 03-22-2012, 08:07 AM

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

artsinyc · 04-13-2012, 04:47 AM

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

sbrohee · 04-16-2012, 04:48 AM

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

sbrohee · 05-02-2012, 06:00 AM

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

sbrohee · 10-30-2012, 04:57 AM

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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03-22-2012, 08:07 AM	#1
sbrohee Member Location: Brussels, Belgium Join Date: Sep 2011 Posts: 19	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

05-02-2012, 06:00 AM	#4
sbrohee Member Location: Brussels, Belgium Join Date: Sep 2011 Posts: 19	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 04:55 AM.

04-13-2012, 04:47 AM	#2
artsinyc Junior Member Location: NY Join Date: Jan 2011 Posts: 1	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

10-30-2012, 04:57 AM	#5
sbrohee Member Location: Brussels, Belgium Join Date: Sep 2011 Posts: 19	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.