bionic (1) fastx_quality_stats.1.gz

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
       (assafgordon@gmail.com)

              [-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.