Question: Trinity assmbly result check
0
gravatar for iamtuttu5
4.5 years ago by
iamtuttu540
United States
iamtuttu540 wrote:

Hello all,

I was running trinity tool , the assembly completed successfully , and i checked the assembly statistics , and obtained this result

 

################################
## Counts of transcripts, etc.
################################
Total trinity 'genes':  2248
Total trinity transcripts:      3471
Percent GC: 50.06

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

        Contig N10: 676
        Contig N20: 483
        Contig N30: 391
        Contig N40: 337
        Contig N50: 299

        Median contig length: 263
        Average contig: 313.58
        Total assembled bases: 1088422


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

        Contig N10: 639
        Contig N20: 439
        Contig N30: 351
        Contig N40: 311
        Contig N50: 279

        Median contig length: 250.5
        Average contig: 299.60
        Total assembled bases: 673498

 

I would like to know whether its a good assembly ?

 

Thank you all

 

 

 

ADD COMMENTlink modified 4.5 years ago by 5heikki8.7k • written 4.5 years ago by iamtuttu540
0
gravatar for 5heikki
4.5 years ago by
5heikki8.7k
Finland
5heikki8.7k wrote:

Whether it's a good assembly or not depends on multiple factors such as the source of your RNA-seq data as well as the applied library preparation protocol. Your average contig/transcript size is ca. 300 nt (100 aa). I would say that this is a pretty average size for prokaryote proteins.

ADD COMMENTlink written 4.5 years ago by 5heikki8.7k

Thank you so much :)

ADD REPLYlink written 4.5 years ago by iamtuttu540

Dear heikki

We are working on plant transcriptome data .. so then also its a reliable result ?.. we are working on trinity for the first time and also new to ngs analysis ..

ADD REPLYlink written 4.5 years ago by iamtuttu540

Perhaps you should check the average transcript size for the most closely related species for which data is available..

ADD REPLYlink written 4.5 years ago by 5heikki8.7k

Thank you heikki .. :)

ADD REPLYlink written 4.5 years ago by iamtuttu540
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