Hey guys, I have raw sequence which had been sequenced on Ion Torrent machine. I had followed the pipeline provided for Ion-torrent sequences and I had also done with denoise-single command with same parameters mentioned in the pipeline. When I ran the command with denoise-pyro it took longer time and when I done with denoise-single it took some time, I have two questions
A) Why the denoise-pyro took longer time.?
B) When I compared both the results there was only an small change in the frequency so can we conclude that we can either commands…? (i.e can we use denoise-single with parameter p-trim-left 15 and use the representative sequences for further analysis)
I am new to Bioinfomatics analysis especially QIIME2
Great question! While denoise-pyro and denoise-single both run on forward reads, they have different settings optimized for the error model of Ion Torrent vs Illumina.
For Illumina, the Q-score represents the chance of a point mutation, like ATT -> GTT.
For Ion Torrent, the Q-score represents the chance of an insertion or deletion, like ATT -> AAATT.
These different settings lead to different run times.
Because you observe the results to be similar, that seems OK to me... But I can see reviewer #3 asking why you didn't used denoise-pyro on your Ion Torrent reads. Probably safer to use the defaults, unless you have positive controls to show the methods are equally good! Do you have any positive controls on this run?
Hey @colinbrislawn Thank you so much for the reply, No,I don’t have an positive control, Infact I had downloaded the sequences from an study…! I think it’s safe to run with denoise-pyro then…!
Probably safer to use the defaults, unless you have positive controls to show the methods are equally good! Do you have any positive controls on this run? 