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

Hello all

I performed trinity assembly using  two fastq files of 3 GB each and obtained result as Trinity.fasta

But result is just 1269 KB in size

Why is it that small ?

Whether there is any problem with assembly ?

 

Any help will be appreciated

Thank you

rna-seq next-gen assembly • 1.2k views
ADD COMMENTlink modified 3.6 years ago by rtliu2.0k • written 3.6 years ago by iamtuttu540

What organism? Did you perform quality checks on your fastq? Did you examine Trinity logs?

ADD REPLYlink written 3.6 years ago by h.mon26k

plant transcriptome data ...

trinity log means ?

 

ADD REPLYlink written 3.6 years ago by iamtuttu540

this is the basic statistics of the obtained result

################################
## Counts of transcripts, etc.
################################
Total trinity 'genes':  2030
Total trinity transcripts:      2723
Percent GC: 49.94

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

        Contig N10: 712
        Contig N20: 504
        Contig N30: 405
        Contig N40: 342
        Contig N50: 303

        Median contig length: 264
        Average contig: 318.96
        Total assembled bases: 868526


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

        Contig N10: 754
        Contig N20: 489
        Contig N30: 377
        Contig N40: 323
        Contig N50: 289

        Median contig length: 257
        Average contig: 310.82
        Total assembled bases: 630964

 

ADD REPLYlink written 3.6 years ago by iamtuttu540
1
gravatar for rtliu
3.6 years ago by
rtliu2.0k
New Zealand
rtliu2.0k wrote:

Supposed you have done proper QC of fastq files (e.g. removing sequencing adaptors),  try normalize reads and assemble the transcript with normalized reads (default 50x coverage): 

Trinity --normalize_reads --seqType fq ...

Trinity Insilico Normalization

 

ADD COMMENTlink written 3.6 years ago by rtliu2.0k
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