summary.qual
The summary.qual command reads a quality file and an optional name, and summarizes the quality information.
Default settings
You must provide a quality file.
mothur > summary.qual(qfile=summary.qual(qfile=stool.trim.pick.qual)
This command will produce a stool.trim.pick.qual.summary, which should look like:
Position numSeqs AverageQ q0 q1 q2 ... q38 q39 q40
0 1382 27.972504 0 0 0 0 ... 11 0 4
1 1382 28.861795 0 0 0 0 ... 27 0 7
2 1382 29.931982 0 0 0 0 ... 28 0 21
3 1382 30.389292 0 0 0 0 ... 32 0 21
4 1382 31.139652 0 0 0 0 ... 53 0 23
5 1382 31.574530 0 0 0 0 ... 66 0 33
6 1382 32.063675 0 0 0 0 ... 85 0 45
7 1382 32.369755 0 0 0 0 ... 97 0 47
8 1382 32.812592 0 0 0 0 ... 110 0 75
9 1382 32.984081 0 0 0 0 ... 132 0 68
...
Position - spot in sequence.
numSeqs - the number of sequence that had that position.
AverageQ - the average quality score
q0 - the number of sequence with a quality score of 0.
q1 - the number of sequence with a quality score of 1.
q2 - the number of sequence with a quality score of 2.
q3 - the number of sequence with a quality score of 3.
q4 - the number of sequence with a quality score of 4.
q5 - the number of sequence with a quality score of 5.
...
...
q40 - the number of sequence with a quality score of 40.
name
The name parameter allows you add a name file with your quality file.
mothur > summary.qual(qfile=stool.trim.pick.qual, name=stool.trim.unique.good.filter.names)
The screen output looks like:
Position NumSeqs AverageQ
0 2382 27.678001
100 2382 36.780018
200 2040 37.163727
count
The count file is similar to the name file in that it is used to represent the number of duplicate sequences for a given representative sequence. It can also contain group information.
mothur > summary.qual(qfile=stool.trim.pick.qual, count=stool.trim.unique.good.filter.count_table)
processors
The processors option enables you to accelerate the alignment by using multiple processors. Default processors=Autodetect number of available processors and use all available.
Revisions
- 1.23.0 First Introduced.
- 1.28.0 Added count option
- 1.40.0 Rewrite of threaded code. Default processors=Autodetect number of available processors and use all available.