---
name: "fastx_quality_stats"
section: "1"
platform: "linux"
package: "fastx-toolkit"
version: "0.0.14-6"
release: "Debian 10 (Buster)"
platforms: ["linux"]
url: "https://new.carta.tech/fastx_quality_stats"
---

# fastx\_quality\_stats(1)

FASTX Statistics

## NAME

fastx\_quality\_stats - FASTX Statistics

## DESCRIPTION

usage: fastx\_quality\_stats \[-h\] \[-N\] \[-i INFILE\] \[-o OUTFILE\] Part of FASTX Toolkit 0.0.14 by A. Gordon (assafgordon@gmail.com)

-

  \[-h\] = This helpful help screen. \[-i INFILE\]  = FASTQ input file. default is STDIN. \[-o OUTFILE\] = TEXT output file. default is STDOUT. \[-N\]         = New output format (with more information per nucleotide/cycle). \[-Q N\]       = FASTQ ASCII offset. Default is 33.

### The \*OLD\* output TEXT file will have the following fields (one row per column):

- column

  \= column number (1 to 36 for a 36-cycles read solexa file)

- count

  \= number of bases found in this column.

- min

  \= Lowest quality score value found in this column.

- max

  \= Highest quality score value found in this column.

- sum

  \= Sum of quality score values for this column.

- mean

  \= Mean quality score value for this column.

- Q1

  \= 1st quartile quality score.

- med

  \= Median quality score.

- Q3

  \= 3rd quartile quality score.

- IQR

  \= Inter-Quartile range (Q3-Q1).

- lW

  \= 'Left-Whisker' value (for boxplotting).

- rW

  \= 'Right-Whisker' value (for boxplotting).

-

  A\_Count = Count of 'A' nucleotides found in this column. C\_Count = Count of 'C' nucleotides found in this column. G\_Count = Count of 'G' nucleotides found in this column. T\_Count = Count of 'T' nucleotides found in this column. N\_Count = Count of 'N' nucleotides found in this column. max-count = max. number of bases (in all cycles)

### The \*NEW\* output format:

-

  cycle (previously called 'column') = cycle number max-count For each nucleotide in the cycle (ALL/A/C/G/T/N):

- count

  \= number of bases found in this column.

- min

  \= Lowest quality score value found in this column.

- max

  \= Highest quality score value found in this column.

- sum

  \= Sum of quality score values for this column.

- mean

  \= Mean quality score value for this column.

- Q1

  \= 1st quartile quality score.

- med

  \= Median quality score.

- Q3

  \= 3rd quartile quality score.

- IQR

  \= Inter-Quartile range (Q3-Q1).

- lW

  \= 'Left-Whisker' value (for boxplotting).

- rW

  \= 'Right-Whisker' value (for boxplotting).

## SEE ALSO

The quality of this automatically generated manpage might be insufficient.  It is suggested to visit

-

  http://hannonlab.cshl.edu/fastx\_toolkit/commandline.html

to get a better layout as well as an overview about connected FASTX tools.