Dear author,
First of all, I would like to thank you for providing this novel and interesting analysis tools, however, I do have some questions.
-
Paired-ended fastq data
I have read the paper and tutorial but it did not mention which one to choose (or I missed it), do you have any suggestion?
I have tested both ended data , and the results are not completely the same. My guess is since the quality of forward ended is higher in general, so I used forward ended fastq file, or do you have other suggestions?
-
The similarity matrix problem
I tested the software in my own mgs data, somehow I discovered that the matrix is like below:
For example
A B C D
100 12 15 25
10 100 20 43
13 17 100 32
23 45 31 100
As my understanding, the value is pairwise distance similarity, so the row name should be
A B C D as well, but we can see that the values in row and column do not exactly match, it is similar but not consistent. like in row A, A to B is 12, but in column A, A to B is 10
If you can help me to get through these issues, I will be much appreciated.
Thank you very much
Dear author,
First of all, I would like to thank you for providing this novel and interesting analysis tools, however, I do have some questions.
Paired-ended fastq data
I have read the paper and tutorial but it did not mention which one to choose (or I missed it), do you have any suggestion?
I have tested both ended data , and the results are not completely the same. My guess is since the quality of forward ended is higher in general, so I used forward ended fastq file, or do you have other suggestions?
The similarity matrix problem
I tested the software in my own mgs data, somehow I discovered that the matrix is like below:
For example
A B C D
100 12 15 25
10 100 20 43
13 17 100 32
23 45 31 100
As my understanding, the value is pairwise distance similarity, so the row name should be
A B C D as well, but we can see that the values in row and column do not exactly match, it is similar but not consistent. like in row A, A to B is 12, but in column A, A to B is 10
If you can help me to get through these issues, I will be much appreciated.
Thank you very much