NAME¶
fastx_quality_stats - FASTX Statistics
DESCRIPTION¶
usage: fastx_quality_stats [-h] [-N] [-i INFILE] [-o OUTFILE] Part of FASTX
Toolkit 0.0.13.2 by A. Gordon (gordon@cshl.edu)
- [-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).
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)
- 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.