No understand the these parameters' concept


(Meha) #1

Dear Friends and colleagues,
Regarding the two these parameters in the qiime dada2 denoise-paired method, I understand the meaning of parents and thread’s concepts. Could you please assist me to learn them?

–p-min-fold-parent-over-abundance FLOAT
The minimum abundance of potential parents
of a sequence being tested as chimeric,
expressed as a fold-change versus the
abundance of the sequence being tested.
Values should be greater than or equal to 1
(i.e. parents should be more abundant than
the sequence being tested). This parameter
has no effect if chimera_method is “none”.
[default: 1.0]
–p-n-threads INTEGER The number of threads to use for
multithreaded processing. If 0 is provided,
all available cores will be used. [default:
1]

Thanks a lot


#2

Hi!
–p-min-fold-parent-over-abundance
The minimum amount of sequences that can be considered as a parent sequence for chimeric sequences (as a result of an error during PCR, for example).
–p-n- threads INTEGER
Here you can indicate how many threads will be involved in your analysis. If you have 20 threads on your machine, you can indicate 16 for this job and you will have 4 for other tasks. If 0 - all threads will be used (faster, but you can’t run something else). If you are skipping this parameter - only one thread will be used (slow, but in this way, it will not take a lot of resources from your machine).


(Meha) #3

Specially thanks for the Qiime2 team for the quick response!
I have a problem with the two terms because they are new to me. What I absorbed your explanation a parent is a representative for CHIMERA or a bad sequence. If I am mistaken, please correct me.

The next word is the thread you. you gladly put info on it, but I do not still know what is a thread. If it is possible, enlighten me, please.

Thank you so much


#4

On your working machine, go to settings - details (Ubuntu) and it will show you how many of threads do you have in processor section. The more you have, the more powerful is your machine. It allows to run some processes in parallel, speeding up the whole process, but taking more resources from your local machine.
Parent is a possible origin sequence of some part of chimeric sequence.


(Meha) #5

Screenshot%20from%202019-02-25%2015-13-40

The present numbers do not show integers like 20 or 4!
Would you mind telling me who many threads I have?


#6

You have 4 threads. 20 I used like an example.


(Meha) #7

Regarding to the mentioned case, I would like to learn what number is typically used for the parameter?

–p-min-fold-parent-over-abundance FLOAT
The minimum abundance of potential parents
of a sequence being tested as chimeric,
expressed as a fold-change versus the
abundance of the sequence being tested.
Values should be greater than or equal to 1
(i.e. parents should be more abundant than
the sequence being tested). This parameter
has no effect if chimera_method is “none”.
[default: 1.0]

I read this page content but I did not catch any number to use. In the description, I am told to use a digit greater than one but How can I know the number should be written?

Have you got any idea?

I took the parameter from:
https://docs.qiime2.org/2019.1/plugins/available/dada2/denoise-paired/

Thanks


#8

You can just skip it. Default meaning is 1.0, that’s good enough for most of the cases, unless you want to indicate another meaning. Since you don’t know what to put, just ignore this one.