Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • 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

  • #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
      Exploring the Dynamics of the Tumor Microenvironment
      by seqadmin




      The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...
      07-08-2024, 03:19 PM
    • seqadmin
      Exploring Human Diversity Through Large-Scale Omics
      by seqadmin


      In 2003, researchers from the Human Genome Project (HGP) announced the most comprehensive genome to date1. Although the genome wasn’t fully completed until nearly 20 years later2, numerous large-scale projects, such as the International HapMap Project and 1000 Genomes Project, continued the HGP's work, capturing extensive variation and genomic diversity within humans. Recently, newer initiatives have significantly increased in scale and expanded beyond genomics, offering a more detailed...
      06-25-2024, 06:43 AM

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, 07-10-2024, 07:30 AM
    0 responses
    26 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 07-03-2024, 09:45 AM
    0 responses
    201 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 07-03-2024, 08:54 AM
    0 responses
    212 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 07-02-2024, 03:00 PM
    0 responses
    193 views
    0 likes
    Last Post seqadmin  
    Working...
    X