Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • SAM platform values

    The SAM read group header line (RG) has a PL tag defined as "platform/technology used to produce the read". It doesn't list a controlled vocabulary.

    Hunting through the GATK source code I see cases where it checks for "ILLUMINA", "solid" and "LS454" - in those uppercase/lowercase manners. Is this as about official as it gets? Is there a more complete list or synonyms anywhere?

    Ideally this should become an official controlled vocabulary.

  • #2
    Originally posted by jkbonfield View Post
    The SAM read group header line (RG) has a PL tag defined as "platform/technology used to produce the read". It doesn't list a controlled vocabulary.

    Hunting through the GATK source code I see cases where it checks for "ILLUMINA", "solid" and "LS454" - in those uppercase/lowercase manners. Is this as about official as it gets? Is there a more complete list or synonyms anywhere?

    Ideally this should become an official controlled vocabulary.
    Check out the headers used in the 1000 Genomes Project. They should have all three technologies represented.

    Comment


    • #3
      Originally posted by nilshomer View Post
      Check out the headers used in the 1000 Genomes Project. They should have all three technologies represented.
      Thanks for the idea, I'll do that.

      However "all three" is already a fail. I can think of (in order of age) capillary/sanger, 454, illumina, solid, not to mention prototypes from new instruments.

      Although 1000 Genomes has not used any capillary data, we do have quite a few mixed assemblies here with old Sanger sequencing data augmented with a mix of newer technologies.

      James

      Comment


      • #4
        Originally posted by jkbonfield View Post
        Thanks for the idea, I'll do that.

        However "all three" is already a fail. I can think of (in order of age) capillary/sanger, 454, illumina, solid, not to mention prototypes from new instruments.

        Although 1000 Genomes has not used any capillary data, we do have quite a few mixed assemblies here with old Sanger sequencing data augmented with a mix of newer technologies.

        James
        Hey now, I meant all three as in all three you mentioned. Don't spark a flame.

        Comment


        • #5
          Sorry, I didn't mean it as a flame. :-)

          Just for the record I'm using "Sanger" as the tag for the sanger sequencing method, although it's a bit generic as it'd catch ABI capillary, licor, megabace etc. They all share similar properties as far as error models go so I think it's sufficient.

          It would be good to get these codified in the SAM spec though.

          James

          Comment

          Latest Articles

          Collapse

          • seqadmin
            Genetic Variation in Immunogenetics and Antibody Diversity
            by seqadmin



            The field of immunogenetics explores how genetic variations influence immune responses and susceptibility to disease. In a recent SEQanswers webinar, Oscar Rodriguez, Ph.D., Postdoctoral Researcher at the University of Louisville, and Ruben Martínez Barricarte, Ph.D., Assistant Professor of Medicine at Vanderbilt University, shared recent advancements in immunogenetics. This article discusses their research on genetic variation in antibody loci, antibody production processes,...
            Yesterday, 07:24 PM
          • seqadmin
            Choosing Between NGS and qPCR
            by seqadmin



            Next-generation sequencing (NGS) and quantitative polymerase chain reaction (qPCR) are essential techniques for investigating the genome, transcriptome, and epigenome. In many cases, choosing the appropriate technique is straightforward, but in others, it can be more challenging to determine the most effective option. A simple distinction is that smaller, more focused projects are typically better suited for qPCR, while larger, more complex datasets benefit from NGS. However,...
            10-18-2024, 07:11 AM

          ad_right_rmr

          Collapse

          News

          Collapse

          Topics Statistics Last Post
          Started by seqadmin, 11-01-2024, 06:09 AM
          0 responses
          24 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 10-30-2024, 05:31 AM
          0 responses
          21 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 10-24-2024, 06:58 AM
          0 responses
          25 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 10-23-2024, 08:43 AM
          0 responses
          56 views
          0 likes
          Last Post seqadmin  
          Working...
          X