Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • metatranscriptome mapping

    Hello!
    I'm sorry for the silly question, but it's the my first time managing metatranscriptomic data and I'm still confused. I have Illumina shotgun metatranscriptome from my samples. I used bowtie to map each sample to some reference genomes from NCBI and so I obtained one .sam file for each sample. My question is... how should I proceed now? I mean, what are the next steps? Moreover, how can I evaluate the quality of the mapping?
    Thanks!!

  • #2
    Try a denovo transcriptome assembly with oases or a similar tool? The program will build contigs that represent transcripts. Use blast2go to annotate those transcripts. Figure out how many organisms you got in each sample.

    Try some tblastx between samples to see what genes are expressed in some samples but not others.

    Comment


    • #3
      Hi Adrian!
      What I'd like to obtain is a sort of table with the gene annotations and the relative abundance in each sample. Starting from my sam files, how could I get this?
      I'm sorry, but I'm quite confused!

      Comment

      Latest Articles

      Collapse

      • seqadmin
        Recent Advances in Sequencing Analysis Tools
        by seqadmin


        The sequencing world is rapidly changing due to declining costs, enhanced accuracies, and the advent of newer, cutting-edge instruments. Equally important to these developments are improvements in sequencing analysis, a process that converts vast amounts of raw data into a comprehensible and meaningful form. This complex task requires expertise and the right analysis tools. In this article, we highlight the progress and innovation in sequencing analysis by reviewing several of the...
        05-06-2024, 07:48 AM
      • seqadmin
        Essential Discoveries and Tools in Epitranscriptomics
        by seqadmin




        The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...
        04-22-2024, 07:01 AM

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by seqadmin, 05-14-2024, 07:03 AM
      0 responses
      19 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 05-10-2024, 06:35 AM
      0 responses
      44 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 05-09-2024, 02:46 PM
      0 responses
      54 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 05-07-2024, 06:57 AM
      0 responses
      42 views
      0 likes
      Last Post seqadmin  
      Working...
      X