man fastx_quality_stats (1): 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).

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).