I have used Trinity 2.8.4 to do denovo assembly of my plant RNA seq data. Now I have finished assembly, but how to know that this denovo assembly is really good and what are all the stats I should consider?
N50 value is 2865 Total trinity 'genes':72392 Total trinity transcripts: 146848 Median contig length: 1071 Average contig: 1664.26 Total assembled bases: 244393103
Does this look good?
copy/pasted from : https://github.com/trinityrnaseq/trinityrnaseq/wiki/Transcriptome-Assembly-Quality-Assessment
"You can see that the Nx values based on the single longest isoform per gene are lower than the Nx stats based on all assembled contigs, as expected, and even though the Nx statistic is really not a reliable indicator of the quality of a transcriptome assembly, the Nx value based on using the longest isoform per gene is perhaps better for reasons described above". (emphasis is mine)