Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • 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

    Comment


    • #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?

              Comment

              Latest Articles

              Collapse

              • seqadmin
                Techniques and Challenges in Conservation Genomics
                by seqadmin



                The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

                Avian Conservation
                Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
                03-08-2024, 10:41 AM
              • 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

              ad_right_rmr

              Collapse

              News

              Collapse

              Topics Statistics Last Post
              Started by seqadmin, 03-14-2024, 06:13 AM
              0 responses
              33 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 03-08-2024, 08:03 AM
              0 responses
              72 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 03-07-2024, 08:13 AM
              0 responses
              81 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 03-06-2024, 09:51 AM
              0 responses
              68 views
              0 likes
              Last Post seqadmin  
              Working...
              X