Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • How to make great wiggle plots and Seq figures

    Hi,

    Does anyone have suggestions for software that easily generate great publication quality figures to display custom tracks - specifically wiggle plots of RNASeq data? The UCSC browser custom tracks are OK, but fuzzy if you try to build figures and IGV from the Broad seems better, but lacks a nice display of splice variants and a clear Y axis.

    Thanks for any help.

    Chris

  • #2
    I really like nimblegen's SignalMap for graphic representation. It can't open HUGE gff/bed files, but the default settings make some nice graphs.

    Comment


    • #3
      Thank you. I will give that a try!

      Chris

      Comment


      • #4
        UCSC isn't fuzzy if you use the PDF/PS link to export postscript. You can edit postscript files with something like Adobe Illustrator to make pretty nice figures.

        You could also make your own figures using R, either with your own code or using something like the GenomeGraphs package.

        Comment


        • #5
          Thanks, I will try that. I didn't know about that feature.

          Chris

          Comment


          • #6
            Hi all,

            I have question on how to plot wiggle tracks. I just have a wig file and a reference genome fasta. Can anyone suggest me some ways i can plot the wiggle into a nice figure.

            Thanks in advance
            Deepak

            Comment

            Latest Articles

            Collapse

            • seqadmin
              The Impact of AI in Genomic Medicine
              by seqadmin



              Artificial intelligence (AI) has evolved from a futuristic vision to a mainstream technology, highlighted by the introduction of tools like OpenAI's ChatGPT and Google's Gemini. In recent years, AI has become increasingly integrated into the field of genomics. This integration has enabled new scientific discoveries while simultaneously raising important ethical questions1. Interviews with two researchers at the center of this intersection provide insightful perspectives into...
              02-26-2024, 02:07 PM
            • seqadmin
              Multiomics Techniques Advancing Disease Research
              by seqadmin


              New and advanced multiomics tools and technologies have opened new avenues of research and markedly enhanced various disciplines such as disease research and precision medicine1. The practice of merging diverse data from various ‘omes increasingly provides a more holistic understanding of biological systems. As Maddison Masaeli, Co-Founder and CEO at Deepcell, aptly noted, “You can't explain biology in its complex form with one modality.”

              A major leap in the field has
              ...
              02-08-2024, 06:33 AM

            ad_right_rmr

            Collapse

            News

            Collapse

            Topics Statistics Last Post
            Started by seqadmin, 02-28-2024, 06:12 AM
            0 responses
            23 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 02-23-2024, 04:11 PM
            0 responses
            70 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 02-21-2024, 08:52 AM
            0 responses
            79 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 02-20-2024, 08:57 AM
            0 responses
            68 views
            0 likes
            Last Post seqadmin  
            Working...
            X