This is the command fastx_quality_stats that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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).
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).
Use fastx_quality_stats online using onworks.net services
