Seqanswers Leaderboard Ad

Collapse
X
 
  • Filter
  • Time
  • Show
Clear All
new posts
  • Giorgio
    Junior Member
    • Oct 2010
    • 4

    Trinity assembly validation and statistics

    Hi All,

    After one week Trinity finally completed an assembly starting with 800 million reads (an entire Next Seq 500 run). The statistics are weird, although there were tons of sequences, but I would like your opinion:

    ################################

    ## Counts of transcripts, etc.

    ################################

    Total trinity 'genes': 858807

    Total trinity transcripts: 924905

    Percent GC: 40.20



    ########################################

    Stats based on ALL transcript contigs:

    ########################################



    Contig N10: 1739

    Contig N20: 769

    Contig N30: 490

    Contig N40: 382

    Contig N50: 324



    Median contig length: 270

    Average contig: 363.98

    Total assembled bases: 336649200





    #####################################################

    ## Stats based on ONLY LONGEST ISOFORM per 'GENE':

    #####################################################



    Contig N10: 1123

    Contig N20: 575

    Contig N30: 421

    Contig N40: 349

    Contig N50: 304



    Median contig length: 268

    Average contig: 341.45

    Total assembled bases: 293239534

    I used Trinity with default parameters and using --trimmomatic plus --min_kmer_cov 2. I really was expecting the N50 to be bigger. What can be the reason for that?

    Note: Before starting the assembly I quality filtered the sequences and merged the results in two big paired end fasta files.



    Please any advice can be precious!

    Thanks!

    Giorgio
  • sarika01
    Junior Member
    • May 2015
    • 2

    #2
    hello I
    I have used trinity for assembly..it give trinity.fatsa file and have 4785 sequences...but whn i run statics program it shown 5000 genes...pls help wht does it mean.

    Comment

    Latest Articles

    Collapse

    • seqadmin
      Pathogen Surveillance with Advanced Genomic Tools
      by seqadmin




      The COVID-19 pandemic highlighted the need for proactive pathogen surveillance systems. As ongoing threats like avian influenza and newly emerging infections continue to pose risks, researchers are working to improve how quickly and accurately pathogens can be identified and tracked. In a recent SEQanswers webinar, two experts discussed how next-generation sequencing (NGS) and machine learning are shaping efforts to monitor viral variation and trace the origins of infectious...
      03-24-2025, 11:48 AM
    • seqadmin
      New Genomics Tools and Methods Shared at AGBT 2025
      by seqadmin


      This year’s Advances in Genome Biology and Technology (AGBT) General Meeting commemorated the 25th anniversary of the event at its original venue on Marco Island, Florida. While this year’s event didn’t include high-profile musical performances, the industry announcements and cutting-edge research still drew the attention of leading scientists.

      The Headliner
      The biggest announcement was Roche stepping back into the sequencing platform market. In the years since...
      03-03-2025, 01:39 PM

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, 03-20-2025, 05:03 AM
    0 responses
    49 views
    0 reactions
    Last Post seqadmin  
    Started by seqadmin, 03-19-2025, 07:27 AM
    0 responses
    57 views
    0 reactions
    Last Post seqadmin  
    Started by seqadmin, 03-18-2025, 12:50 PM
    0 responses
    50 views
    0 reactions
    Last Post seqadmin  
    Started by seqadmin, 03-03-2025, 01:15 PM
    0 responses
    201 views
    0 reactions
    Last Post seqadmin  
    Working...