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  • captainentropy
    replied
    No, you don't need Galaxy. What harryzs posted (directly from the ngsplot website) is correct.

    I'm using ngsplot and I do not have Galaxy installed on my server.

    Leave a comment:


  • paolo.kunder
    replied
    I think you need to install it,
    anyway some other suggestions?

    Leave a comment:


  • harryzs
    replied
    Originally posted by paolo.kunder View Post
    Honestly I would like to avoid installing Galaxy in my server, any other suggestion?
    I don't think you need to install Galaxy.

    Code:
     A user only needs to write a very small configuration file, telling the program which samples to look at and how they should be combined with different regions, and then run the program with one command line. A web-based version (Galaxy) of ngs.plot is also developed to be used by wet-lab biologists who tend to be averse to command line usage.

    Leave a comment:


  • Michael.Ante
    replied
    Hi Paolo,

    have you tried Ensembl's Perl API in combination with the Bioperl's Samtools?
    A nice tutorial can be found here.

    Leave a comment:


  • paolo.kunder
    replied
    Honestly I would like to avoid installing Galaxy in my server, any other suggestion?

    Leave a comment:


  • harryzs
    replied
    try ngsplot

    Quick mining and visualization of NGS data by integrating genomic databases - shenlab-sinai/ngsplot

    Leave a comment:


  • paolo.kunder
    started a topic tag density distribution over the gene body

    tag density distribution over the gene body

    Dear All,

    I have a bam file of a MeDIP seq sample.
    I have also a bed file of all mouse genes.

    I would like to plot the tag density over the genebody as illustrated in this two examples I found in the literature.

    I know how to plot the tag density distribution relative to the TSS and +2kb/-2kb both, but how do I deal with the gene body?

    Many Thanks,
    Paolo
    Attached Files

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