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  • 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.

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