.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.43.3.
.TH FASTX_QUALITY_STATS "1" "January 2014" "fastx_quality_stats 0.0.14" "User Commands"
.SH NAME
fastx_quality_stats \- FASTX Statistics
.SH DESCRIPTION
usage: fastx_quality_stats [\-h] [\-N] [\-i INFILE] [\-o OUTFILE]
Part of FASTX Toolkit 0.0.14 by A. Gordon (assafgordon@gmail.com)
.IP
[\-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).
.SS "The *OLD* output TEXT file will have the following fields (one row per column):"
.TP
column
= column number (1 to 36 for a 36\-cycles read solexa file)
.TP
count
= number of bases found in this column.
.TP
min
= Lowest quality score value found in this column.
.TP
max
= Highest quality score value found in this column.
.TP
sum
= Sum of quality score values for this column.
.TP
mean
= Mean quality score value for this column.
.TP
Q1
= 1st quartile quality score.
.TP
med
= Median quality score.
.TP
Q3
= 3rd quartile quality score.
.TP
IQR
= Inter\-Quartile range (Q3\-Q1).
.TP
lW
= 'Left\-Whisker' value (for boxplotting).
.TP
rW
= 'Right\-Whisker' value (for boxplotting).
.IP
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)
.SS "The *NEW* output format:"
.IP
cycle (previously called 'column') = cycle number
max\-count
For each nucleotide in the cycle (ALL/A/C/G/T/N):
.TP
count
= number of bases found in this column.
.TP
min
= Lowest quality score value found in this column.
.TP
max
= Highest quality score value found in this column.
.TP
sum
= Sum of quality score values for this column.
.TP
mean
= Mean quality score value for this column.
.TP
Q1
= 1st quartile quality score.
.TP
med
= Median quality score.
.TP
Q3
= 3rd quartile quality score.
.TP
IQR
= Inter\-Quartile range (Q3\-Q1).
.TP
lW
= 'Left\-Whisker' value (for boxplotting).
.TP
rW
= 'Right\-Whisker' value (for boxplotting).
.SH SEE ALSO
The quality of this automatically generated manpage might be
insufficient.  It is suggested to visit
.IP
http://hannonlab.cshl.edu/fastx_toolkit/commandline.html
.P
to get a better layout as well as an overview about connected
FASTX tools.