SUMMARISING RUN PARAMETERS ========================== Input filename: N1-M-iG-IgG_S10_L003_R2_001.fastq.gz Trimming mode: single-end Trim Galore version: 0.4.4 Cutadapt version: 1.18 Quality Phred score cutoff: 0 Quality encoding type selected: ASCII+33 Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; user defined) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length before a sequence gets removed: 20 bp Output file will be GZIP compressed This is cutadapt 1.18 with Python 2.7.13 Command line parameters: -f fastq -e 0.1 -q 0 -O 1 -a CTGTCTCTTATA N1-M-iG-IgG_S10_L003_R2_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 46.46 s (24 us/read; 2.45 M reads/minute). === Summary === Total reads processed: 1,900,828 Reads with adapters: 1,709,721 (89.9%) Reads written (passing filters): 1,900,828 (100.0%) Total basepairs processed: 287,025,028 bp Quality-trimmed: 0 bp (0.0%) Total written (filtered): 153,979,582 bp (53.6%) === Adapter 1 === Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 1709721 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 7.0% C: 49.0% G: 25.6% T: 16.4% none/other: 2.1% Overview of removed sequences length count expect max.err error counts 1 65650 475207.0 0 65650 2 22609 118801.8 0 22609 3 8432 29700.4 0 8432 4 4642 7425.1 0 4642 5 3549 1856.3 0 3549 6 2423 464.1 0 2423 7 2332 116.0 0 2332 8 2361 29.0 0 2361 9 2204 7.3 0 2201 3 10 2572 1.8 1 2367 205 11 2463 0.5 1 2417 46 12 3503 0.1 1 3378 125 13 3726 0.1 1 3654 72 14 4376 0.1 1 4292 84 15 3985 0.1 1 3905 80 16 3285 0.1 1 3220 65 17 3125 0.1 1 3062 63 18 2053 0.1 1 2012 41 19 2941 0.1 1 2905 36 20 2699 0.1 1 2605 94 21 2732 0.1 1 2698 34 22 4425 0.1 1 4319 106 23 4271 0.1 1 4189 82 24 6897 0.1 1 6756 141 25 5251 0.1 1 5112 139 26 5772 0.1 1 5608 164 27 3828 0.1 1 3762 66 28 2978 0.1 1 2878 100 29 2640 0.1 1 2580 60 30 3129 0.1 1 3067 62 31 3102 0.1 1 2998 104 32 4467 0.1 1 4353 114 33 4944 0.1 1 4877 67 34 6963 0.1 1 6827 136 35 7503 0.1 1 7373 130 36 7298 0.1 1 7175 123 37 5683 0.1 1 5587 96 38 4288 0.1 1 4204 84 39 3816 0.1 1 3752 64 40 3109 0.1 1 3025 84 41 3732 0.1 1 3667 65 42 5342 0.1 1 5248 94 43 5911 0.1 1 5796 115 44 7971 0.1 1 7863 108 45 9979 0.1 1 9805 174 46 7961 0.1 1 7806 155 47 7377 0.1 1 7226 151 48 5542 0.1 1 5456 86 49 4625 0.1 1 4548 77 50 3371 0.1 1 3344 27 51 4201 0.1 1 4157 44 52 4735 0.1 1 4646 89 53 6962 0.1 1 6882 80 54 10482 0.1 1 10269 213 55 12773 0.1 1 12636 137 56 13737 0.1 1 13584 153 57 11861 0.1 1 11656 205 58 9536 0.1 1 9299 237 59 7035 0.1 1 6903 132 60 4577 0.1 1 4523 54 61 4427 0.1 1 4386 41 62 5822 0.1 1 5755 67 63 8639 0.1 1 8515 124 64 13259 0.1 1 13088 171 65 16936 0.1 1 16673 263 66 19343 0.1 1 19033 310 67 19737 0.1 1 19436 301 68 16194 0.1 1 16017 177 69 10894 0.1 1 10793 101 70 7648 0.1 1 7471 177 71 5790 0.1 1 5730 60 72 7329 0.1 1 7247 82 73 11955 0.1 1 11798 157 74 17185 0.1 1 17021 164 75 25610 0.1 1 25352 258 76 31988 0.1 1 31714 274 77 32248 0.1 1 31913 335 78 28408 0.1 1 28026 382 79 22799 0.1 1 22416 383 80 14255 0.1 1 14046 209 81 10441 0.1 1 10347 94 82 9332 0.1 1 9252 80 83 13157 0.1 1 13033 124 84 24501 0.1 1 24273 228 85 32084 0.1 1 31751 333 86 45022 0.1 1 44426 596 87 56785 0.1 1 56161 624 88 48468 0.1 1 47931 537 89 38511 0.1 1 38065 446 90 24553 0.1 1 24275 278 91 15817 0.1 1 15654 163 92 11034 0.1 1 10975 59 93 11073 0.1 1 10970 103 94 22152 0.1 1 21861 291 95 35908 0.1 1 35503 405 96 53553 0.1 1 52982 571 97 66117 0.1 1 65296 821 98 64960 0.1 1 64306 654 99 51042 0.1 1 50592 450 100 37894 0.1 1 37367 527 101 22284 0.1 1 21902 382 102 13614 0.1 1 13342 272 103 11389 0.1 1 11297 92 104 14929 0.1 1 14760 169 105 23127 0.1 1 22771 356 106 32886 0.1 1 32506 380 107 41392 0.1 1 40859 533 108 39296 0.1 1 39001 295 109 28407 0.1 1 28260 147 110 20043 0.1 1 19810 233 111 12450 0.1 1 12342 108 112 7303 0.1 1 7243 60 113 3676 0.1 1 3653 23 114 3349 0.1 1 3328 21 115 3461 0.1 1 3414 47 116 2377 0.1 1 2354 23 117 2574 0.1 1 2540 34 118 3603 0.1 1 3579 24 119 1704 0.1 1 1692 12 120 1179 0.1 1 1164 15 121 450 0.1 1 445 5 122 651 0.1 1 621 30 123 91 0.1 1 89 2 124 107 0.1 1 80 27 125 93 0.1 1 88 5 126 71 0.1 1 51 20 127 45 0.1 1 43 2 128 37 0.1 1 33 4 129 1 0.1 1 1 130 5 0.1 1 2 3 131 5 0.1 1 0 5 132 36 0.1 1 12 24 133 2 0.1 1 2 134 16 0.1 1 1 15 136 1 0.1 1 1 139 1 0.1 1 0 1 141 199 0.1 1 196 3 142 1 0.1 1 0 1 143 2 0.1 1 0 2 147 1 0.1 1 0 1 148 13 0.1 1 1 12 149 33 0.1 1 0 33 150 35 0.1 1 35 151 36176 0.1 1 34869 1307 RUN STATISTICS FOR INPUT FILE: N1-M-iG-IgG_S10_L003_R2_001.fastq.gz ============================================= 1900828 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 36516 (1.9%)