SUMMARISING RUN PARAMETERS ========================== Input filename: N1-M-iG-H2A_S8_L003_R1_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-H2A_S8_L003_R1_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 227.66 s (25 us/read; 2.38 M reads/minute). === Summary === Total reads processed: 9,033,159 Reads with adapters: 7,940,913 (87.9%) Reads written (passing filters): 9,033,159 (100.0%) Total basepairs processed: 1,364,007,009 bp Quality-trimmed: 0 bp (0.0%) Total written (filtered): 725,465,977 bp (53.2%) === Adapter 1 === Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 7940913 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 7.1% C: 49.0% G: 26.7% T: 17.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 375505 2258289.8 0 375505 2 126587 564572.4 0 126587 3 47981 141143.1 0 47981 4 23432 35285.8 0 23432 5 15478 8821.4 0 15478 6 14570 2205.4 0 14570 7 14928 551.3 0 14928 8 15577 137.8 0 15577 9 17812 34.5 0 17713 99 10 17666 8.6 1 16561 1105 11 12170 2.2 1 11759 411 12 10473 0.5 1 10088 385 13 10451 0.5 1 10087 364 14 9902 0.5 1 9571 331 15 8848 0.5 1 8533 315 16 8219 0.5 1 7949 270 17 7973 0.5 1 7690 283 18 8439 0.5 1 8174 265 19 10997 0.5 1 10676 321 20 11714 0.5 1 11395 319 21 9665 0.5 1 9378 287 22 10532 0.5 1 10218 314 23 10634 0.5 1 10344 290 24 13898 0.5 1 13476 422 25 11138 0.5 1 10825 313 26 12284 0.5 1 11958 326 27 8652 0.5 1 8406 246 28 7422 0.5 1 7224 198 29 6817 0.5 1 6639 178 30 7248 0.5 1 7060 188 31 7948 0.5 1 7746 202 32 10517 0.5 1 10238 279 33 13279 0.5 1 12947 332 34 15475 0.5 1 15094 381 35 16737 0.5 1 16309 428 36 15458 0.5 1 15028 430 37 13006 0.5 1 12695 311 38 10331 0.5 1 10067 264 39 8265 0.5 1 8078 187 40 7836 0.5 1 7633 203 41 8456 0.5 1 8253 203 42 12154 0.5 1 11900 254 43 16779 0.5 1 16420 359 44 22091 0.5 1 21605 486 45 25141 0.5 1 24621 520 46 25209 0.5 1 24670 539 47 22106 0.5 1 21630 476 48 16907 0.5 1 16504 403 49 12910 0.5 1 12646 264 50 10647 0.5 1 10385 262 51 10964 0.5 1 10709 255 52 15336 0.5 1 15012 324 53 23648 0.5 1 23176 472 54 31322 0.5 1 30696 626 55 39669 0.5 1 38980 689 56 41506 0.5 1 40809 697 57 37915 0.5 1 37296 619 58 31563 0.5 1 31042 521 59 22789 0.5 1 22378 411 60 16801 0.5 1 16475 326 61 14596 0.5 1 14323 273 62 19541 0.5 1 19226 315 63 30517 0.5 1 30029 488 64 46379 0.5 1 45719 660 65 61139 0.5 1 60306 833 66 72501 0.5 1 71371 1130 67 69999 0.5 1 68946 1053 68 58156 0.5 1 57233 923 69 45080 0.5 1 44332 748 70 30963 0.5 1 30454 509 71 22617 0.5 1 22268 349 72 25810 0.5 1 25421 389 73 41030 0.5 1 40384 646 74 67004 0.5 1 65994 1010 75 101853 0.5 1 100465 1388 76 128168 0.5 1 126270 1898 77 131387 0.5 1 129441 1946 78 119468 0.5 1 117925 1543 79 93163 0.5 1 91984 1179 80 64246 0.5 1 63367 879 81 41784 0.5 1 41270 514 82 41012 0.5 1 40404 608 83 50036 0.5 1 49318 718 84 97957 0.5 1 96668 1289 85 144323 0.5 1 142459 1864 86 203906 0.5 1 201407 2499 87 235986 0.5 1 232999 2987 88 225858 0.5 1 222968 2890 89 185506 0.5 1 183150 2356 90 134149 0.5 1 132501 1648 91 87695 0.5 1 86531 1164 92 54332 0.5 1 53547 785 93 57218 0.5 1 56358 860 94 107838 0.5 1 106113 1725 95 186859 0.5 1 183894 2965 96 285995 0.5 1 281580 4415 97 365641 0.5 1 360144 5497 98 377614 0.5 1 372079 5535 99 315468 0.5 1 310642 4826 100 235218 0.5 1 231049 4169 101 143354 0.5 1 140549 2805 102 80341 0.5 1 78890 1451 103 58618 0.5 1 57526 1092 104 86742 0.5 1 85134 1608 105 153809 0.5 1 151475 2334 106 233528 0.5 1 230048 3480 107 272439 0.5 1 268402 4037 108 272988 0.5 1 268882 4106 109 196135 0.5 1 193388 2747 110 125362 0.5 1 123605 1757 111 67856 0.5 1 66927 929 112 31482 0.5 1 31080 402 113 11908 0.5 1 11749 159 114 11463 0.5 1 11255 208 115 12103 0.5 1 11933 170 116 15246 0.5 1 15022 224 117 13853 0.5 1 13664 189 118 17298 0.5 1 17076 222 119 8330 0.5 1 8253 77 120 5623 0.5 1 5518 105 121 2126 0.5 1 2082 44 122 2814 0.5 1 2741 73 123 567 0.5 1 544 23 124 1909 0.5 1 1856 53 125 299 0.5 1 274 25 126 1175 0.5 1 1136 39 127 875 0.5 1 835 40 128 516 0.5 1 482 34 129 95 0.5 1 82 13 130 633 0.5 1 614 19 131 93 0.5 1 64 29 132 132 0.5 1 110 22 133 36 0.5 1 17 19 134 73 0.5 1 11 62 135 20 0.5 1 1 19 136 20 0.5 1 8 12 137 20 0.5 1 6 14 138 18 0.5 1 5 13 139 59 0.5 1 3 56 140 25 0.5 1 5 20 141 34 0.5 1 7 27 142 27 0.5 1 14 13 143 83 0.5 1 17 66 144 15 0.5 1 4 11 145 11 0.5 1 4 7 146 7 0.5 1 4 3 147 8 0.5 1 1 7 148 26 0.5 1 6 20 149 20 0.5 1 2 18 150 1 0.5 1 0 1 151 2909 0.5 1 2832 77 RUN STATISTICS FOR INPUT FILE: N1-M-iG-H2A_S8_L003_R1_001.fastq.gz ============================================= 9033159 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 3544 (0.0%)