by column fastq_stats.py '$input_file' '$output_file' '${input_file.extension[len( 'fastq' ):]}'

This tool creates summary statistics on a FASTQ file. .. class:: infomark **TIP:** This statistics report can be used as input for the **Boxplot** and **Nucleotides Distribution** tools. ----- **The output file will contain the following fields:** * 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). * outliers = Scores falling beyond the left and right whiskers (comma separated list). * 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. * Other_Nucs = Comma separated list of other nucleotides found in this column. * Other_Count = Comma separated count of other nucleotides found in this column. For example:: #column count min max sum mean Q1 med Q3 IQR lW rW outliers A_Count C_Count G_Count T_Count N_Count other_bases other_base_count 1 14336356 2 33 450600675 31.4306281875 32.0 33.0 33.0 1.0 31 33 2,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30 4482314 2199633 4425957 3208745 19707 2 14336356 2 34 441135033 30.7703737965 30.0 33.0 33.0 3.0 26 34 2,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25 4419184 2170537 4627987 3118567 81 3 14336356 2 34 433659182 30.2489127642 29.0 32.0 33.0 4.0 23 34 2,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22 4310988 2941988 3437467 3645784 129 4 14336356 2 34 433635331 30.2472490917 29.0 32.0 33.0 4.0 23 34 2,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22 4110637 3007028 3671749 3546839 103 5 14336356 2 34 432498583 30.167957813 29.0 32.0 33.0 4.0 23 34 2,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22 4348275 2935903 3293025 3759029 124 ----- .. class:: warningmark Adapter bases in color space reads are excluded from statistics.