Comparing Trinity Assembly Results
0
0
Entering edit mode
8.0 years ago

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
RNA-Seq Trinity Assembly • 1.9k views
ADD COMMENT

Login before adding your answer.

Traffic: 1138 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6