Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • The best to process sample with 2 lanes of data?

    Hi, I have pair end illumina RNA seq data, each sample was ran on 2 lanes. What is the best way to process data of this kind? Do I just combine the rawdata or I process them separately?

  • #2
    I had a post discussing this you might find helpful. I dont know how to link it in here so you might search it in my profile.

    Basically, it depends on the type of analysis you are doing.
    Last edited by csoong; 01-06-2011, 01:56 PM.

    Comment


    • #3
      Depends on your computation environment more than anything I'd say. Sometimes its nice to run the alignment in parallel at the same time, one lane at a time, or certain steps are to memory intensive for you enviroment if you put them all together. Sometimes worth testing both to see what works best for you. For instance if you use BWA to align and Samtools I'm not sure which is faster;
      cat lanes together
      bwa aln, sam generation
      samtools sam-->bam, sort, index

      or
      run lanes separate (2 at a time if you can) with
      bwa aln, sam generation
      samtools sam-->bam, sort, merge, index

      so in that example it is a question of if you can run in parallel or not?, do you have enough resources to sort all the lanes together, is samtools merge of parallel runs faster than aln all at once.

      My guess is that running in parallel is much faster if you have the resources to do this, which most standard boxes purchased in the last year (dual hexa-core systems with at least 16Gb ram) should be able to do at least 2 lanes at a time easily

      Comment

      Latest Articles

      Collapse

      • 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
      • 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

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by seqadmin, Yesterday, 06:37 PM
      0 responses
      11 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, Yesterday, 06:07 PM
      0 responses
      10 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-22-2024, 10:03 AM
      0 responses
      51 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-21-2024, 07:32 AM
      0 responses
      68 views
      0 likes
      Last Post seqadmin  
      Working...
      X