Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • annotation of local sequence "uniqueness"

    Hi all-- I am attempting to filter out false "SNPs" in my bowtie assemblies (yeast genomic DNA). One major predictor of SNP falseness is being located in a regions that shows sequence similarity with somewhere else in the genome (e.g., paralogs, telomeres).

    I've attempted to limit the read mismapping that underlies these SNPs by tweaking the bowtie parameters, but I still get quite a few. So an alternative would be to ask, for each region containing a putative SNP, what is the local uniqueness?

    Does anyone know of a previously generated track that catalogs this property? Or better still, a tool that would perform a sliding window analysis (probably by parsing BLAST or BLAT) to record it for any given sequence?

    Thanks!

  • #2
    Wouldn't you be able to infer true positives based on the depth and nucleotide ratios at that position? '

    Since you have the SAM/BAM output you could try varscan (http://varscan.sourceforge.net/) or the samtools pipeline (http://samtools.sourceforge.net/mpileup.shtml). You can filter these SNPs with these tools and they both provide nucleotide resolution for each putative SNP. More so the samtools pipeline, but I prefer varscan sine it is a bit cleaner.

    Comment


    • #3
      Hi Twaddlac--

      Thanks for the reply. I don't think depth can get me all the way. Sometimes the depth is lower than "regular" sequence, but not always. It can also look normal or be higher (which would make sense if reads from two locations in the genome are mapping to the same place). I must tolerate the possibility of real heterozygotes so allele frequency can only do so much, also.

      I am already using SAMtools, but I'll check out varscan, Thanks!

      Comment


      • #4
        The term "mappability" has emerged to refer to this - using this as a search term is likely to yield results. There are a few tools that compute mappability measures, for example GEM: http://sourceforge.net/apps/mediawik...ility_man_page.

        Comment


        • #5
          thanks gaffa, the right search term is exactly what I needed and I didn't know 'mappability'... something definitely wasn't right about "uniqueness". Thanks!

          Comment

          Latest Articles

          Collapse

          • seqadmin
            Latest Developments in Precision Medicine
            by seqadmin



            Technological advances have led to drastic improvements in the field of precision medicine, enabling more personalized approaches to treatment. This article explores four leading groups that are overcoming many of the challenges of genomic profiling and precision medicine through their innovative platforms and technologies.

            Somatic Genomics
            “We have such a tremendous amount of genetic diversity that exists within each of us, and not just between us as individuals,”...
            Today, 01:16 PM
          • seqadmin
            Recent Advances in Sequencing Analysis Tools
            by seqadmin


            The sequencing world is rapidly changing due to declining costs, enhanced accuracies, and the advent of newer, cutting-edge instruments. Equally important to these developments are improvements in sequencing analysis, a process that converts vast amounts of raw data into a comprehensible and meaningful form. This complex task requires expertise and the right analysis tools. In this article, we highlight the progress and innovation in sequencing analysis by reviewing several of the...
            05-06-2024, 07:48 AM

          ad_right_rmr

          Collapse

          News

          Collapse

          Topics Statistics Last Post
          Started by seqadmin, Today, 07:15 AM
          0 responses
          10 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, Yesterday, 10:28 AM
          0 responses
          15 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, Yesterday, 07:35 AM
          0 responses
          16 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 05-22-2024, 02:06 PM
          0 responses
          8 views
          0 likes
          Last Post seqadmin  
          Working...
          X