Entering edit mode
7.4 years ago
tanz.renner
•
0
We just got Trinity 2.3.2 up and running on our HPC and I am comparing the assembly stats to an assembly of the exact same data using a version of Trinity (2014-07-17). I am seeing a big difference in the N50 - any thoughts and which assembly would you use for downstream analyses? Thanks :-)
Trinity 2.3.2 assembly stats:
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## Counts of transcripts, etc.
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Total trinity 'genes': 60875
Total trinity transcripts: 70247
Percent GC: 38.01
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Stats based on ALL transcript contigs:
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Contig N10: 2734
Contig N20: 1949
Contig N30: 1487
Contig N40: 1157
Contig N50: 891
Median contig length: 402
Average contig: 639.82
Total assembled bases: 44945631
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## Stats based on ONLY LONGEST ISOFORM per 'GENE':
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Contig N10: 2371
Contig N20: 1687
Contig N30: 1283
Contig N40: 993
Contig N50: 766
Median contig length: 381
Average contig: 584.98
Total assembled bases: 35610552
**Trinity 2014-07-17 stats:**
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## Counts of transcripts, etc.
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Total trinity 'genes': 58889
Total trinity transcripts: 83365
Percent GC: 36.33
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Stats based on ALL transcript contigs:
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Contig N10: 4540
Contig N20: 3422
Contig N30: 2690
Contig N40: 2161
Contig N50: 1743
Median contig length: 535
Average contig: 987.77
Total assembled bases: 82345048
#####################################################
## Stats based on ONLY LONGEST ISOFORM per 'GENE':
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Contig N10: 4501
Contig N20: 3294
Contig N30: 2545
Contig N40: 2009
Contig N50: 1599
Median contig length: 433
Average contig: 869.64
Total assembled bases: 51212327
