N 50 Value

Question

[ravichandiranbt]

I had Transcriptome sequencing data 2x150 bp reads. I had done quality filtering my data before assembly. For assembly i had used Trinity assembler. But in the output of Trinity I am getting N50 value of 2.5KB. Whether these N50 value is accepted. If not how to reduce it. Thank You.

Answer 1

[WouterDeCoster]

If you would have read more about the N50 value (e.g. a series of blog posts starting with this one), you would know that the higher your N50, the better. However, that's a term mostly used for genome assembly, as for transcriptome assembly you are always limited by the size of your transcripts. You can get longer "contigs" than the transcripts in your transcriptome, of course.

That said, an N50 of 2.5kb for a transcriptome is probably pretty good. If annotation of your species (or similar) is available you could plot your contig/transcript lengths versus the known transcript lengths, and I expect things will be okay. And if not, it will be a lot more informative than looking at the N50 metric.