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 ([email protected])
-
[-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.