Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Where do I start?! Bacterial rRNA sequencing

    Good morning!!!

    I am fairly new to the world of sequencing and bioinformatics! But as part of my PhD I am sequencing 16S rRNA to identify what bacterial consortia are present in some microalgal cultures I have!

    The idea is to do Ion Torrent type sequencing of the V6 region to start identifying the bacterial consortia present.

    From what I understand, we will then receive the raw data as FASTQ ( millions of reads (??)) which we then need to sort through using software such as TopHat then use rRNA databases such as SILVA to place the bacteria in a phylogenetic tree.

    Do any of you have any advice of what software to use and what databases? What parameters must be set for ambiguity so my results are of a publishable quality (cross fingers)?

    Any help to try and understand the bioinformatics side of things will be greatly appreciated!!

    Have a lovely day all!!

  • #2
    You would not be using TopHat for the analysis you describe since it is meant for analysis of expression data.

    You are interested in microbial communities, so Qiime and Mothur will likely be what you will end up using. There are tutorials availalable for Qiime (http://qiime.org/tutorials/) and Mothur (http://www.mothur.org/wiki/Main_Page).

    Comment


    • #3
      Thank you so much for pointing me in the right direction, GenoMax!

      Have a lovely day!

      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
      10 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
      67 views
      0 likes
      Last Post seqadmin  
      Working...
      X