Transcriptome output

Since the last post I have re-run the assembly with both paired and unpaired trimmed sequences. My new transcriptome is not very different in size but I am yet to determine if there are other variations for downstream analysis.

To obtain some statistics of the trinity output you can use the N50 check.

#Run N50 script
/usr/local/trinity/2.1.1/util/TrinityStats.pl AP.fasta

with an output like this:

################################
## Counts of transcripts, etc.
################################
Total trinity ‘genes’: 67231
Total trinity transcripts: 82911
Percent GC: 45.44

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

Contig N10: 3700
Contig N20: 2863
Contig N30: 2350
Contig N40: 1979
Contig N50: 1654

Median contig length: 585
Average contig: 983.42
Total assembled bases: 81535957
#####################################################
## Stats based on ONLY LONGEST ISOFORM per ‘GENE’:
#####################################################

Contig N10: 3463
Contig N20: 2612
Contig N30: 2127
Contig N40: 1758
Contig N50: 1408

Median contig length: 476
Average contig: 834.77
Total assembled bases: 56122482

Compared to previous assembly:

################################
## Counts of transcripts, etc.
################################
Total trinity ‘genes’: 67123
Total trinity transcripts: 82776
Percent GC: 45.44

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

Contig N10: 3687
Contig N20: 2864
Contig N30: 2350
Contig N40: 1978
Contig N50: 1652

Median contig length: 586
Average contig: 983.62
Total assembled bases: 81419959
#####################################################
## Stats based on ONLY LONGEST ISOFORM per ‘GENE’:
#####################################################

Contig N10: 3456
Contig N20: 2612
Contig N30: 2126
Contig N40: 1757
Contig N50: 1407

Median contig length: 476
Average contig: 834.73
Total assembled bases: 56029878

 

 

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out /  Change )

Google photo

You are commenting using your Google account. Log Out /  Change )

Twitter picture

You are commenting using your Twitter account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )

Connecting to %s