fastx_uncollapser(1) [debian man page]

FASTX_UNCOLLAPSER(1)						   User Commands					      FASTX_UNCOLLAPSER(1)

NAME

       fastx_uncollapser - FASTA/Q Uncollapser

DESCRIPTION

       usage: fasta_uncollapser [-c N] [-h] [-v] [-i INFILE] [-o OUTFILE] Part of FASTX Toolkit 0.0.13.2 by A. Gordon (gordon@cshl.edu)

       [-h]   = This helpful help screen.

       [-v]   = verbose: print short summary of input/output counts

       [-c N] = Assume input is a tabular file (not FASTA file),

	      And the collapsed identifier (e.g. '1-1000') is on column N.

       [-i INFILE]
	      = FASTA/Tabular input file. default is STDIN.

	      [-o OUTFILE] = FASTA/Tabular output file. default is STDOUT.

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.

fastx_uncollapser 0.0.13.2					     May 2012						      FASTX_UNCOLLAPSER(1)

FASTX_QUALITY_STATS(1)						   User Commands					    FASTX_QUALITY_STATS(1)

NAME

       fastx_quality_stats - FASTX Statistics

DESCRIPTION

       usage: fastx_quality_stats [-h] [-N] [-i INFILE] [-o OUTFILE] Part of FASTX Toolkit 0.0.13.2 by A. Gordon (gordon@cshl.edu)

	      [-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' nucleo-
	      tides 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.

fastx_quality_stats 0.0.13.2					     May 2012						    FASTX_QUALITY_STATS(1)