SUMMARISING RUN PARAMETERS ========================== Input filename: N1-H-iG-IgG_S10_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-IgG_S10_L002_R1_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 226.41 s (40 us/read; 1.52 M reads/minute). === Summary === Total reads processed: 5,717,719 Reads with adapters: 3,368,580 (58.9%) Reads written (passing filters): 5,717,719 (100.0%) Total basepairs processed: 863,375,569 bp Quality-trimmed: 0 bp (0.0%) Total written (filtered): 725,642,716 bp (84.0%) === Adapter 1 === Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 3368580 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 11.9% C: 44.1% G: 25.0% T: 19.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 894720 1429429.8 0 894720 2 260589 357357.4 0 260589 3 94237 89339.4 0 94237 4 33967 22334.8 0 33967 5 15823 5583.7 0 15823 6 12985 1395.9 0 12985 7 12508 349.0 0 12508 8 11043 87.2 0 11043 9 10082 21.8 0 9906 176 10 13446 5.5 1 12403 1043 11 14649 1.4 1 13779 870 12 12900 0.3 1 12364 536 13 15313 0.3 1 14744 569 14 16985 0.3 1 16372 613 15 14146 0.3 1 13669 477 16 13289 0.3 1 12843 446 17 11838 0.3 1 11408 430 18 10729 0.3 1 10289 440 19 9006 0.3 1 8714 292 20 10411 0.3 1 9974 437 21 12823 0.3 1 12459 364 22 13241 0.3 1 12772 469 23 14718 0.3 1 14184 534 24 15068 0.3 1 14625 443 25 16144 0.3 1 15459 685 26 15596 0.3 1 15098 498 27 13838 0.3 1 13457 381 28 11040 0.3 1 10667 373 29 11135 0.3 1 10718 417 30 10410 0.3 1 10062 348 31 11182 0.3 1 10842 340 32 14058 0.3 1 13629 429 33 17194 0.3 1 16684 510 34 19433 0.3 1 18877 556 35 20357 0.3 1 19808 549 36 16382 0.3 1 15906 476 37 15584 0.3 1 15154 430 38 12730 0.3 1 12359 371 39 10480 0.3 1 10184 296 40 11329 0.3 1 10931 398 41 11444 0.3 1 11139 305 42 13048 0.3 1 12721 327 43 17304 0.3 1 16970 334 44 19988 0.3 1 19517 471 45 22461 0.3 1 21852 609 46 23466 0.3 1 22730 736 47 18830 0.3 1 18397 433 48 14613 0.3 1 14255 358 49 12290 0.3 1 12054 236 50 11287 0.3 1 11066 221 51 11790 0.3 1 11491 299 52 14426 0.3 1 14124 302 53 16720 0.3 1 16349 371 54 23143 0.3 1 22625 518 55 27328 0.3 1 26804 524 56 29068 0.3 1 28321 747 57 25313 0.3 1 24886 427 58 19266 0.3 1 18899 367 59 13195 0.3 1 12969 226 60 11401 0.3 1 11165 236 61 10351 0.3 1 10147 204 62 13232 0.3 1 12939 293 63 17260 0.3 1 16838 422 64 24209 0.3 1 23732 477 65 32387 0.3 1 31823 564 66 33810 0.3 1 33244 566 67 30951 0.3 1 30417 534 68 24223 0.3 1 23851 372 69 19538 0.3 1 19209 329 70 14545 0.3 1 14335 210 71 11558 0.3 1 11363 195 72 11977 0.3 1 11722 255 73 17509 0.3 1 17254 255 74 26767 0.3 1 26336 431 75 33938 0.3 1 33351 587 76 40161 0.3 1 39668 493 77 41289 0.3 1 40761 528 78 34706 0.3 1 34181 525 79 25401 0.3 1 25061 340 80 16828 0.3 1 16561 267 81 13312 0.3 1 13158 154 82 11995 0.3 1 11795 200 83 13922 0.3 1 13662 260 84 23504 0.3 1 23181 323 85 34579 0.3 1 34033 546 86 47906 0.3 1 47198 708 87 51954 0.3 1 51162 792 88 44327 0.3 1 43744 583 89 37015 0.3 1 36527 488 90 22343 0.3 1 21843 500 91 14772 0.3 1 14417 355 92 11880 0.3 1 11638 242 93 13184 0.3 1 13040 144 94 18158 0.3 1 17857 301 95 30238 0.3 1 29875 363 96 39441 0.3 1 38950 491 97 46285 0.3 1 45606 679 98 45816 0.3 1 45282 534 99 32556 0.3 1 32089 467 100 23495 0.3 1 23016 479 101 13527 0.3 1 13246 281 102 9677 0.3 1 9428 249 103 8023 0.3 1 7894 129 104 9957 0.3 1 9844 113 105 15291 0.3 1 15159 132 106 20218 0.3 1 20004 214 107 23164 0.3 1 22934 230 108 21732 0.3 1 21499 233 109 17629 0.3 1 17355 274 110 12292 0.3 1 12087 205 111 7149 0.3 1 7022 127 112 4958 0.3 1 4849 109 113 2458 0.3 1 2408 50 114 2565 0.3 1 2498 67 115 2066 0.3 1 2042 24 116 2168 0.3 1 2113 55 117 2268 0.3 1 2212 56 118 2224 0.3 1 2096 128 119 1124 0.3 1 1039 85 120 782 0.3 1 729 53 121 763 0.3 1 758 5 122 436 0.3 1 401 35 123 427 0.3 1 406 21 124 215 0.3 1 186 29 125 333 0.3 1 156 177 126 17 0.3 1 16 1 127 19 0.3 1 18 1 128 181 0.3 1 30 151 129 66 0.3 1 38 28 130 29 0.3 1 28 1 131 21 0.3 1 4 17 132 84 0.3 1 25 59 133 50 0.3 1 1 49 134 2 0.3 1 0 2 135 54 0.3 1 2 52 136 20 0.3 1 20 137 54 0.3 1 0 54 138 76 0.3 1 0 76 139 373 0.3 1 373 140 6 0.3 1 6 141 87 0.3 1 52 35 142 34 0.3 1 34 143 66 0.3 1 9 57 144 25 0.3 1 0 25 145 75 0.3 1 12 63 146 28 0.3 1 21 7 147 72 0.3 1 65 7 148 44 0.3 1 11 33 149 3 0.3 1 3 150 7 0.3 1 7 151 530 0.3 1 492 38 RUN STATISTICS FOR INPUT FILE: N1-H-iG-IgG_S10_L002_R1_001.fastq.gz ============================================= 5717719 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 1690 (0.0%)