Trinity assmbly result check

Question

[iamtuttu5]

Hello all,

I was running trinity tool, the assembly completed successfully. 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

Answer 1

[5heikki]

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.

[iamtuttu5]

Thank you so much :)

[iamtuttu5]

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 ..

[5heikki]

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

[iamtuttu5]

Thank you heikki .. :)