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  • how to create interval lists for picard?

    Hi,

    I need a rRNA interval list file for picard's CollectRnaSeqMetrics, as defined here. Is there a handy tool to create these from a given annotation file or a source of prebuilt files (for ensembl GRCh37)?
    Last edited by sidderb; 03-20-2012, 09:29 PM.
    @sidderb

  • #2
    co-ask

    co-ask the same question

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    • #3
      Fairly easy though not simply explained:

      Code:
      samtools view -H YourBamAlignedToGenome.bam > header.txt
      cat header.txt ribosome_locations.txt > GRCh37_ribosome_interval_list.txt
      If you need other examples try (http://www.keatslab.org/resources/ngs-tools/ngs-scripts)

      Comment


      • #4
        jon, thx. I checked your website, really helpful. the question i have now is how to create ribosome_locations.txt? thx

        Comment


        • #5
          i mean how to create that file for other species, for example, mouse

          Comment


          • #6
            You can make the header as described here: http://www.broadinstitute.org/gsa/wi...ference_genome

            Then, for your intervals, make lines like:

            chr1 1485 4892 + target_1
            chr2 3490 9400 + target_2

            Everything should be tab-delimited.

            Comment


            • #7
              Is "target_1" etc just referring to the gene? i.e. Can I have the same value repeated multiple times for this column, or does each entry have to be unique? target_1 through target_6000?

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