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  • 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

  • #2
    Hi Sylvain,
    You may want to try our tool for peak profiles and heatmaps:

    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

    Comment


    • #3
      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
      Attached Files

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      • #4
        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, 04:55 AM.

        Comment


        • #5
          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.

          Comment

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