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  • need a Genome browser to view Mb in a window

    I need a genome browser which allows me to view MB or even the whole genome in a window.

    I'm mapping ChipSeq Illumina short reads to a genome. I want to see a distribution of numbers of matches across a chromosome. I've tried IGV. However, it only let me view up to 70Kb in a window. When I further zoom out, I can not see any distribution nor sequences any more.

    Please suggest a genome browser fit my purpose. Thanks!!

  • #2
    SeqMonk would certainly be up for the task.

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    • #3
      UCSC Browser can visualize whole chromosomes. Circos may vizualize whole genomes if u manage to compile it (i had no success on my mac).

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      • #4
        Generate a bigWig (or even just a wig or bedgraph if you're just talking about 1Mb) from your bam file and then plug it into UCSC Genome Browser or IGV.
        Mendelian Disorder: A blogshare of random useful information for general public consumption. [Blog]
        Breakway: A Program to Identify Structural Variations in Genomic Data [Website] [Forum Post]
        Projects: U87MG whole genome sequence [Website] [Paper]

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        • #5
          2 questions:

          1. How to generate a bigWig from a bam file?

          2. can UCSC Genome Browser be installed and run on a local machine?

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          • #6
            Originally posted by shuang View Post
            2. can UCSC Genome Browser be installed and run on a local machine?
            Yes, here is the link to install UCSC genome browser
            http://genome.ucsc.edu/admin/jk-install.html

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            • #7
              Originally posted by shuang View Post
              1. How to generate a bigWig from a bam file?
              Try BEDtools. Also: http://seqanswers.com/forums/showthread.php?t=7379
              Mendelian Disorder: A blogshare of random useful information for general public consumption. [Blog]
              Breakway: A Program to Identify Structural Variations in Genomic Data [Website] [Forum Post]
              Projects: U87MG whole genome sequence [Website] [Paper]

              Comment


              • #8
                I tried to follow this workflow to generate a BigWig. However, what is
                "chromsizes.txt" in step 3 and 4.

                Thanks!!


                Workflow:
                # 1. Convert SAM to BAM
                samtools view -S -b -o sample.bam sample.sam
                # 2. Sort the BAM file
                samtools sort sample.bam sample.sorted
                # 3. Create BedGraph coverage file
                genomeCoverageBed -bg -ibam sample.sorted.bam -g chromsizes.txt > sample.bedgraph
                # 4. Convert the BedGraph file to BigWig
                bedGraphToBigWig sample.bedgraph chromsizes.txt sample.bw

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