SUMMARISING RUN PARAMETERS ========================== Input filename: N1-H-iG-H2A_S8_L002_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-H-iG-H2A_S8_L002_R1_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 242.77 s (35 us/read; 1.70 M reads/minute). === Summary === Total reads processed: 6,897,700 Reads with adapters: 4,566,172 (66.2%) Reads written (passing filters): 6,897,700 (100.0%) Total basepairs processed: 1,041,552,700 bp Quality-trimmed: 0 bp (0.0%) Total written (filtered): 783,800,241 bp (75.3%) === Adapter 1 === Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 4566172 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 9.9% C: 47.0% G: 26.3% T: 16.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 956462 1724425.0 0 956462 2 279364 431106.2 0 279364 3 111931 107776.6 0 111931 4 37055 26944.1 0 37055 5 20123 6736.0 0 20123 6 17405 1684.0 0 17405 7 17284 421.0 0 17284 8 18069 105.3 0 18069 9 19201 26.3 0 19019 182 10 19162 6.6 1 17758 1404 11 13195 1.6 1 12443 752 12 9947 0.4 1 9460 487 13 10085 0.4 1 9593 492 14 8919 0.4 1 8488 431 15 7483 0.4 1 7109 374 16 7657 0.4 1 7282 375 17 7062 0.4 1 6742 320 18 8100 0.4 1 7739 361 19 10038 0.4 1 9569 469 20 11034 0.4 1 10544 490 21 9347 0.4 1 8947 400 22 8086 0.4 1 7724 362 23 8339 0.4 1 7972 367 24 8631 0.4 1 8262 369 25 8028 0.4 1 7706 322 26 7203 0.4 1 6921 282 27 6214 0.4 1 5944 270 28 5414 0.4 1 5215 199 29 5486 0.4 1 5250 236 30 5653 0.4 1 5423 230 31 6453 0.4 1 6224 229 32 7501 0.4 1 7211 290 33 9544 0.4 1 9220 324 34 10621 0.4 1 10248 373 35 10729 0.4 1 10336 393 36 9700 0.4 1 9338 362 37 8259 0.4 1 7977 282 38 6724 0.4 1 6491 233 39 5717 0.4 1 5491 226 40 5780 0.4 1 5582 198 41 6675 0.4 1 6474 201 42 8354 0.4 1 8096 258 43 11292 0.4 1 10979 313 44 13563 0.4 1 13156 407 45 15262 0.4 1 14857 405 46 15492 0.4 1 15080 412 47 13350 0.4 1 12972 378 48 10114 0.4 1 9805 309 49 7849 0.4 1 7602 247 50 6703 0.4 1 6484 219 51 7873 0.4 1 7657 216 52 9957 0.4 1 9685 272 53 13521 0.4 1 13165 356 54 18712 0.4 1 18264 448 55 22291 0.4 1 21784 507 56 23583 0.4 1 23009 574 57 21359 0.4 1 20831 528 58 16823 0.4 1 16446 377 59 11805 0.4 1 11513 292 60 9260 0.4 1 9006 254 61 8855 0.4 1 8621 234 62 11440 0.4 1 11171 269 63 16936 0.4 1 16481 455 64 25781 0.4 1 25192 589 65 32120 0.4 1 31444 676 66 36834 0.4 1 36038 796 67 35144 0.4 1 34392 752 68 28169 0.4 1 27632 537 69 20856 0.4 1 20436 420 70 15223 0.4 1 14925 298 71 11169 0.4 1 10942 227 72 13427 0.4 1 13183 244 73 19701 0.4 1 19325 376 74 32557 0.4 1 32006 551 75 45231 0.4 1 44539 692 76 53742 0.4 1 52812 930 77 58101 0.4 1 57069 1032 78 50583 0.4 1 49706 877 79 39778 0.4 1 39084 694 80 28352 0.4 1 27829 523 81 17683 0.4 1 17350 333 82 16051 0.4 1 15722 329 83 20466 0.4 1 20106 360 84 37487 0.4 1 36834 653 85 60415 0.4 1 59305 1110 86 84233 0.4 1 82759 1474 87 100509 0.4 1 98813 1696 88 90065 0.4 1 88512 1553 89 72446 0.4 1 71226 1220 90 48728 0.4 1 47868 860 91 30938 0.4 1 30448 490 92 20911 0.4 1 20492 419 93 23118 0.4 1 22711 407 94 41446 0.4 1 40756 690 95 70982 0.4 1 69838 1144 96 103308 0.4 1 101642 1666 97 129777 0.4 1 127784 1993 98 129592 0.4 1 127656 1936 99 108846 0.4 1 107165 1681 100 78920 0.4 1 77684 1236 101 49572 0.4 1 48842 730 102 27932 0.4 1 27524 408 103 19726 0.4 1 19438 288 104 29733 0.4 1 29243 490 105 53429 0.4 1 52626 803 106 79814 0.4 1 78701 1113 107 93939 0.4 1 92705 1234 108 95011 0.4 1 93703 1308 109 78059 0.4 1 76999 1060 110 55024 0.4 1 54224 800 111 33144 0.4 1 32691 453 112 16035 0.4 1 15794 241 113 6720 0.4 1 6598 122 114 5641 0.4 1 5537 104 115 7744 0.4 1 7633 111 116 8012 0.4 1 7858 154 117 8385 0.4 1 8250 135 118 9106 0.4 1 8922 184 119 5508 0.4 1 5413 95 120 2701 0.4 1 2637 64 121 1408 0.4 1 1371 37 122 916 0.4 1 894 22 123 327 0.4 1 269 58 124 149 0.4 1 126 23 125 87 0.4 1 48 39 126 42 0.4 1 30 12 127 77 0.4 1 46 31 128 56 0.4 1 8 48 129 37 0.4 1 10 27 130 34 0.4 1 13 21 131 28 0.4 1 5 23 132 49 0.4 1 23 26 133 65 0.4 1 11 54 134 25 0.4 1 5 20 135 34 0.4 1 4 30 136 23 0.4 1 1 22 137 22 0.4 1 5 17 138 34 0.4 1 1 33 139 27 0.4 1 3 24 140 12 0.4 1 0 12 141 71 0.4 1 10 61 142 33 0.4 1 8 25 143 150 0.4 1 10 140 144 13 0.4 1 2 11 145 22 0.4 1 1 21 146 10 0.4 1 2 8 147 12 0.4 1 3 9 148 43 0.4 1 5 38 149 11 0.4 1 1 10 150 8 0.4 1 1 7 151 349 0.4 1 345 4 RUN STATISTICS FOR INPUT FILE: N1-H-iG-H2A_S8_L002_R1_001.fastq.gz ============================================= 6897700 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 1013 (0.0%)