Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Newbie to MiSeq, QIIME workflow question

    Hi all,

    I just got my MiSeq data for fungal ITS sequences in a large number of samples. I am going to be using QIIME to do the analysis and I have a basic workflow from another person, but I wasn't sure about where paired end assembly would be in the workflow.

    I know that MiSeq data is already demultiplexed and that I will be using the split_libraries_fastq.py function, but do I need to do paired end assembly before that? What program is best to use for that, PANDASeq or join_paired_ends.py? For each sample I have two FASTQ files, Read 1 and Read 2, but the workflow I have does not address that.

    Thanks

  • #2
    Here's my processing script for getting already demultiplexed sequences to the point of running through qiime. The for loop makes sense for the way that I name my samples/sequences, but may not make sense for your naming convention.

    Microbial ecologist, running a sequencing core. I have lots of strong opinions on how to survey communities, pretty sure some are even correct.

    Comment


    • #3
      Originally posted by rc630 View Post
      I know that MiSeq data is already demultiplexed and that I will be using the split_libraries_fastq.py function, but do I need to do paired end assembly before that? What program is best to use for that, PANDASeq or join_paired_ends.py?
      Yes, you should merge the paired reads into single reads. The best program for that purpose is BBMerge.

      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, 03-27-2024, 06:37 PM
      0 responses
      12 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-27-2024, 06:07 PM
      0 responses
      11 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-22-2024, 10:03 AM
      0 responses
      53 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-21-2024, 07:32 AM
      0 responses
      69 views
      0 likes
      Last Post seqadmin  
      Working...
      X