Question: Comparing Trinity Assembly Results
0
gravatar for tanz.renner
2.9 years ago by
tanz.renner0 wrote:

We just got Trinity 2.3.2 up and running on our HPC and I am comparing the assembly stats to an assembly of the exact same data using a version of Trinity (2014-07-17). I am seeing a big difference in the N50 - any thoughts and which assembly would you use for downstream analyses? Thanks :-)

Trinity 2.3.2 assembly stats:

################################
## Counts of transcripts, etc.
################################
Total trinity 'genes':  60875
Total trinity transcripts:  70247
Percent GC: 38.01

########################################
Stats based on ALL transcript contigs:
########################################

        Contig N10: 2734
        Contig N20: 1949
        Contig N30: 1487
        Contig N40: 1157
        Contig N50: 891

        Median contig length: 402
        Average contig: 639.82
        Total assembled bases: 44945631


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

        Contig N10: 2371
        Contig N20: 1687
        Contig N30: 1283
        Contig N40: 993
        Contig N50: 766

        Median contig length: 381
        Average contig: 584.98
        Total assembled bases: 35610552

**Trinity 2014-07-17 stats:** 

################################
## Counts of transcripts, etc.
################################
Total trinity 'genes':  58889
Total trinity transcripts:  83365
Percent GC: 36.33

########################################
Stats based on ALL transcript contigs:
########################################

    Contig N10: 4540
    Contig N20: 3422
    Contig N30: 2690
    Contig N40: 2161
    Contig N50: 1743

    Median contig length: 535
    Average contig: 987.77
    Total assembled bases: 82345048


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

    Contig N10: 4501
    Contig N20: 3294
    Contig N30: 2545
    Contig N40: 2009
    Contig N50: 1599

    Median contig length: 433
    Average contig: 869.64
    Total assembled bases: 51212327
assembly rna-seq trinity • 946 views
ADD COMMENTlink modified 2.9 years ago by genomax73k • written 2.9 years ago by tanz.renner0
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