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).

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):