Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • running TopHat with ~1.2 billion reads

    Any tips for the quickest way to get TopHat to complete alignment of a very large dataset (~1.2 billion 75bp Single end HiSeq reads)? I considered splitting it into 10 but then realized this would risk treating identical reads in the ten subsets as unique in the final file. I'm looking to keep anything that maps up to 10 locations, with up to three mismatches and three bp indels:
    Code:
     -p 16 -g 10 --read-mismatches 3 --read-gap-length 3 --read-edit-dist 3
    .

    Thanks,

    Shurjo

  • #2
    Split it, and dedup it later?

    Comment


    • #3
      Do you have to use Tophat?
      STAR will do split read alignment in a small fraction of the time that it takes Tophat.

      Comment


      • #4
        GPU option

        SOAP3-dp is very fast as long as you are ok with only up to 4 mismatches.

        Comment


        • #5
          All of these sound very logical. I'm going to step out of my TopHat-based comfort zone and try STAR and SOAP3-dp.

          ECO, nice to see the forum doing so well. I've been away from this world for a bit but am coming back soon.

          Thanks everyone,

          Shurjo

          Comment


          • #6
            Shurjo: nice to see you back here. Always wished I'd been able to follow our collaboration through. Good luck in your current work.

            Comment

            Latest Articles

            Collapse

            • seqadmin
              Current Approaches to Protein Sequencing
              by seqadmin


              Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...
              04-04-2024, 04:25 PM
            • seqadmin
              Strategies for Sequencing Challenging Samples
              by seqadmin


              Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
              03-22-2024, 06:39 AM

            ad_right_rmr

            Collapse

            News

            Collapse

            Topics Statistics Last Post
            Started by seqadmin, 04-11-2024, 12:08 PM
            0 responses
            14 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 04-10-2024, 10:19 PM
            0 responses
            19 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 04-10-2024, 09:21 AM
            0 responses
            16 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 04-04-2024, 09:00 AM
            0 responses
            43 views
            0 likes
            Last Post seqadmin  
            Working...
            X