Question: Normalizing CAZy data
0
gravatar for mss
21 months ago by
mss30
mss30 wrote:

Hi,

I am annotating two fungal genomes. I have run the genomes through dbCAN database to determine how many of the putative proteins encode CAZy enzymes, but now I am trying to figure out if I can simply report the relative abundance of the genes for each genome, or if I need to show some sort of normalization of the number of enzymes?

Many papers that I have read normalize their reads in some way, but I believe that this is because these are based off transcripts, not a "near" complete genome.

Like shown here in figure 2:

https://www.researchgate.net/publication/320565582_Predicted_microbial_secretomes_and_their_target_substrates_in_marine_sediment/figures?lo=1&utm_source=google&utm_medium=organic

or here: https://www.frontiersin.org/files/Articles/313095/fmicb-09-00299-HTML/image_m/fmicb-09-00299-g002.jpg

I hope this makes sense. Please share your thoughts.

Thanks in advance! Morgan

ADD COMMENTlink written 21 months ago by mss30
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1485 users visited in the last hour