Parameters are done In Order?


(Meha) #1

Hi friends,

I would like to know sth. Does Qiime2 perform the parameters sequentially?

e.g. Does Qiime2 firstly perform trim then trunc-len parameters in this command? Or all parameters are done simultaneously?
Also, changing the parameters’ places from up to down or vice versa has affect on the result?

qiime dada2 denoise-paired
–i-demultiplexed-seqs demux.qza
–p-trim-left-f 13 *
** --p-trim-left-r 13 *

–p-trunc-len-f 150 *
** --p-trunc-len-r 150 *

–o-table table.qza
–o-representative-sequences rep-seqs.qza
–o-denoising-stats denoising-stats.qza

Thanks


(Nicholas Bokulich) #2

No, the order in which you write the parameters does not impact the order in which they are performed.

Any command will perform several steps under the hood in a prescribed order. Whenever the order is significant, the command’s help documentation often describes the order. The order they appear in the help documentation is usually arbitrary and does not reflect the order of their use.

In the case of the trim and trunc parameters, it truncates first, then trims.


(Meha) #3

Is it ok if I unable trunc parameter and do trimming first. The next step I truncate the reads, filtering reads that are smaller than the desired ones. If the truncing is performed firstly based on your opinion, I will lose a lot of reads in this circumstance. Given that I thought to implement this way. I do not know it is suitable or not!

Admittedly my PCR amplicon is longer that’s why I have lower amount of merging reads. I mean overlapping area is in minority. I am going to ask you weather the method I mentioned is technically not problematic? if no, do you suggest it? i can use single-end plugins and methods but I insist in using paired end reads for the most reliable result.

What is your idea?


(Nicholas Bokulich) #4

You cannot change the order in which QIIME 2 performs these steps.