Trinity assembly validation and statistics

[Giorgio]

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, although there were tons of sequences, but I would like your opinion:

################################

## Counts of transcripts, etc.

################################

Total trinity 'genes': 858807

Total trinity transcripts: 924905

Percent GC: 40.20



########################################

Stats based on ALL transcript contigs:

########################################



Contig N10: 1739

Contig N20: 769

Contig N30: 490

Contig N40: 382

Contig N50: 324



Median contig length: 270

Average contig: 363.98

Total assembled bases: 336649200





#####################################################

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

#####################################################



Contig N10: 1123

Contig N20: 575

Contig N30: 421

Contig N40: 349

Contig N50: 304



Median contig length: 268

Average contig: 341.45

Total assembled bases: 293239534

I used Trinity with default parameters and using --trimmomatic plus --min_kmer_cov 2. I really was expecting the N50 to be bigger. What can be the reason for that?

Note: Before starting the assembly I quality filtered the sequences and merged the results in two big paired end fasta files.



Please any advice can be precious!

Thanks!

Giorgio

[sarika01]

hello I
I have used trinity for assembly..it give trinity.fatsa file and have 4785 sequences...but whn i run statics program it shown 5000 genes...pls help wht does it mean.