Comparing Trinity Assembly Results

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

• 2,224 views • link

updated 9.7 years ago by GenoMax

• written 9.7 years ago by tanz.renner •

0 answers

No answers yet.

More posts like this

Total trinity genes, Total trinity transcripts ad unigene
written 2.6 years ago by sansan •

Hello, I am new to transcriptomic analysis and I want to understand what "Total trinity 'genes'" and "Total trinity transcripts" mean in an assembly generated …
BUSCO duplicated
written 2.6 years ago by san96 •

Hello everyone, I just assembled a data set from a non-model organism with Trinity, however, I am getting many contigs. I ran cd-hit to remove …
how to merge two files in two columns using bash command lines
written 5.1 years ago by FadyNabil •

I have these two files: the first one looks like that: ################################ ## Counts of transcripts, etc. ################################ Total trinity 'genes': 2478 Total trinity transcripts: …
RNA de novo assembly - blasts - KEGG - GO
written 6.4 years ago by dimitrischat

Hello, I am a phd candidate to bioninformatics and with (almost) 0 guidance. Seeking help here.. I was asked to do a de novo RNA …
assessing de novo Trinity assembly quality
written 10.1 years ago by trish0401 •

I used Trinity to make a de novo transcriptome assembly for 1 human sample (I will be using more samples later, this is just the …
Trinity, longest contigs
written 10.5 years ago by loly.pearl86 •

Hi All, Can some one explain to me how can I generate the longest and shortest contigs length from this trinity assembly summary: ``` ################################ …
Trinity predicting more number of genes?
written 10.6 years ago by kanika.151

``` ################################ ## Counts of transcripts, etc. ################################ Total trinity 'genes': 35868 Total trinity transcripts: 54969 Percent GC: 51.52 ######################################## Stats based on ALL transcript …
Trinity assmbly result check
written 10.7 years ago by iamtuttu5 •

Hello all, I was running trinity tool, the assembly completed successfully. I checked the assembly statistics and obtained this result ``` ################################ ## Counts of …
Cleaning up trinity assemblies
written 10.9 years ago by dpearton •

Hi, I have performed de novo assemblies on mRNA using trinity with PE illumina data (125bp PE). Trinity gives a large number of contigs (around …
Trinity assembly validation and statistics
written 11.3 years ago by giorgiocasaburi

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, …