Seqanswers Leaderboard Ad

Collapse
X
 
  • Filter
  • Time
  • Show
Clear All
new posts
  • gevielr
    Member
    • Oct 2013
    • 14

    discarding homopolymer reads

    I'm looking for a script that I could use to remove all homopolymer reads from my 100 bp PE reads. These are unusually overabundant in my sample.

    I can't seem to find a script that will do this. I've tried to use fastx_clipper, but defining the adapter as a homopolymer, and that didn't work (defined adaptor too long?).

    Any ideas?
  • lethalfang
    Member
    • Aug 2011
    • 95

    #2
    Originally posted by gevielr View Post
    I'm looking for a script that I could use to remove all homopolymer reads from my 100 bp PE reads. These are unusually overabundant in my sample.

    I can't seem to find a script that will do this. I've tried to use fastx_clipper, but defining the adapter as a homopolymer, and that didn't work (defined adaptor too long?).

    Any ideas?
    I wrote a script in python3 that does that. You may find that useful. If you're interested, email me [email protected]

    Comment

    • gevielr
      Member
      • Oct 2013
      • 14

      #3
      Great, thanks!! I'll shoot you an email.

      Comment

      • Wallysb01
        Senior Member
        • Feb 2011
        • 286

        #4
        You could also use dust via prinseq. You might have to play around with the scoring to get a sense of the type of reads you're losing, but it should become pretty clear when you're dumping only very low complexity stuff, like say trinucleotide repeats and shorter.

        Comment

        • bfantinatti
          Member
          • Aug 2012
          • 22

          #5
          Dust

          I am using DUST to perform this task.
          But DUST do not remove the reads with low complexity. It put the low complexity bases in lowercase.
          I don't know how to remove those lowercase reads after running DUST.

          How do you guys do to remove those reads after running DUST?

          Comment

          Latest Articles

          Collapse

          • seqadmin
            New Genomics Tools and Methods Shared at AGBT 2025
            by seqadmin


            This year’s Advances in Genome Biology and Technology (AGBT) General Meeting commemorated the 25th anniversary of the event at its original venue on Marco Island, Florida. While this year’s event didn’t include high-profile musical performances, the industry announcements and cutting-edge research still drew the attention of leading scientists.

            The Headliner
            The biggest announcement was Roche stepping back into the sequencing platform market. In the years since...
            03-03-2025, 01:39 PM
          • seqadmin
            Investigating the Gut Microbiome Through Diet and Spatial Biology
            by seqadmin




            The human gut contains trillions of microorganisms that impact digestion, immune functions, and overall health1. Despite major breakthroughs, we’re only beginning to understand the full extent of the microbiome’s influence on health and disease. Advances in next-generation sequencing and spatial biology have opened new windows into this complex environment, yet many questions remain. This article highlights two recent studies exploring how diet influences microbial...
            02-24-2025, 06:31 AM

          ad_right_rmr

          Collapse

          News

          Collapse

          Topics Statistics Last Post
          Started by seqadmin, Today, 05:03 AM
          0 responses
          15 views
          0 reactions
          Last Post seqadmin  
          Started by seqadmin, Yesterday, 07:27 AM
          0 responses
          12 views
          0 reactions
          Last Post seqadmin  
          Started by seqadmin, 03-18-2025, 12:50 PM
          0 responses
          14 views
          0 reactions
          Last Post seqadmin  
          Started by seqadmin, 03-03-2025, 01:15 PM
          0 responses
          185 views
          0 reactions
          Last Post seqadmin  
          Working...