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UNIX for Dummies Questions & Answers
How to sum rows in e.g. column 1 by a category in e.g. column 2
Post 302415581 by Scrutinizer on Friday 23rd of April 2010 01:39:13 AM
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LEARN ABOUT DEBIAN
fastx_quality_stats
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)