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  • visualizing scripture output BED

    Hi,

    I'm working through an analysis with Scripture for the first time.

    I've been able to generate a bed and dot file. UCSC does not seem like this BED file.

    I was able to find this suggestion that scripture includes a gff converter:



    java -Xmx1000m -jar <path_to_scripture>/scripture.jar -task toGFF -cufflinks -in scripture.t0.bed -source SCRIPTURE -out scripture.t0.gtf -prefix t0

    but... this toGFF function does not seem to be described in the scripture documentation, and does not seem to work for me either.

    Any suggestions? All I am really trying to do is to get this into UCSC so I can quickly assess how things look. Scripture suggests IGV browser which I suppose I could also use.

    thanks!

  • #2
    What happens when you try upload the .bed file to the UCSC browser?

    Comment


    • #3
      error message

      I get this:

      Code:
      File 'allScores.bed' - Unrecognized format line 1 of custom track: chr1	199	249	chr1:199-249	0.0	*	199	249	0,0,0	1	50,	0,	1.0	0.3684297339584846	1.0	0.02 3.1075660687968516	0.0542844351489113	50.0	1.0 (note: chrom names are case sensitive)
      thoughts? Maybe I need some sort of header?

      generally the scripture documentation seems somewhat half written, unless I am missing something?

      Comment


      • #4
        fyi, the chromosome name is fine... (no caps problem there)

        Comment


        • #5
          Hi,

          I have been able to open bed files in UCSC Genome browser using Scripture-beta2 version and this type of command:

          java -Xmx2000m -jar scripture-beta2.jar -task extractDot -in Segmentation_Results/chr1.scriptureESTest.segments.graph.post.add.pairs.dot -chr chr1 -start 6235241 -end 6239548 -out chr1_6235241-6239548.dot

          It gives a dot file and a bed file for the indicated region of the chromosome.
          Hope this help !

          Emilie
          Last edited by Emilie; 01-26-2011, 05:57 AM.

          Comment


          • #6
            .bed files don't require a header, but you can include one. Bed format instructions:
            http://genome.ucsc.edu/FAQ/FAQformat#format1
            I think you have too many columns in your file. Can you post the first few lines from your file, exactly as written in the file?

            Comment


            • #7
              Originally posted by chrisbala View Post
              Hi,

              I'm working through an analysis with Scripture for the first time.

              I've been able to generate a bed and dot file. UCSC does not seem like this BED file.

              I was able to find this suggestion that scripture includes a gff converter:



              java -Xmx1000m -jar <path_to_scripture>/scripture.jar -task toGFF -cufflinks -in scripture.t0.bed -source SCRIPTURE -out scripture.t0.gtf -prefix t0

              but... this toGFF function does not seem to be described in the scripture documentation, and does not seem to work for me either.

              Any suggestions? All I am really trying to do is to get this into UCSC so I can quickly assess how things look. Scripture suggests IGV browser which I suppose I could also use.

              thanks!
              Would you tell me that how can you transfer the bed file from scripture to gtf file please?

              Comment

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