How to find the number of contigs produced? N50 length in base pairs? N90 length in base pairs? I am having trouble with some underlying questions about my project.
I have ran a Trinity tool to create a trinity.fasta file.
To determine some underlying questions, I used the utility asm_stats to gather some basic statistics.
I am just having some issues of calculating data.
DATA:
Main genome scaffold N/L50: 7464/1.032 KB
Main genome contig N/L50: 7464/1.032 KB
Main genome scaffold N/L90: 14314/106
Main genome contig N/L90: 14314/106
Number of contigs (scaffold length):
25,534 (ALL)
25,534 (100)
21,609 (250)
10,818 (500)
907 (1 KB)
38 (2.5KB)
5 (5 KB)
2 (10KB)
With the data attached above, would my N50 and N90 length in BASE PAIRS so excluding the kb, be 7464 and 14314, respectively?
Would the number of contigs produced by this assembly be 7, since there are 7 different contigs produced or would it be 25,534?
Thanks!
With the data attached above, would my N50 and N90 length in BASE PAIRS so excluding the kb, be 7464 and 14314, respectively?

Looks like this is inverse so your N50 is 1032bp and your N90 is 106bp. N90 cannot be longer than N50 by definition. You L50 and L90 are 7464 and 14314

Would the number of contigs produced by this assembly be 7, since there are 7 different contigs produced or would it be 25,534?

25534
Now for the real answer. Do not calculate or report N50 on transcript assemblies. It is more than useless. Transcriptomes are - by nature - dynamic in length. Longer is not better in this regard. Are your short transcripts lower quality assemblies, probably not, but N50 treats them as such. Please read the Trinity wiki for other, better ways to QC your transcript assembly.