SUMMARISING RUN PARAMETERS ========================== Input filename: N1-H-iG-H2A_S8_L002_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-H-iG-H2A_S8_L002_R2_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 243.34 s (35 us/read; 1.70 M reads/minute). === Summary === Total reads processed: 6,897,700 Reads with adapters: 4,586,377 (66.5%) 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): 784,593,715 bp (75.3%) === Adapter 1 === Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 4586377 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 9.9% C: 47.8% G: 25.7% T: 16.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 987352 1724425.0 0 987352 2 280480 431106.2 0 280480 3 112103 107776.6 0 112103 4 37175 26944.1 0 37175 5 20242 6736.0 0 20242 6 17850 1684.0 0 17850 7 17456 421.0 0 17456 8 18059 105.3 0 18059 9 19192 26.3 0 19013 179 10 18752 6.6 1 17008 1744 11 13072 1.6 1 12455 617 12 9825 0.4 1 9352 473 13 9991 0.4 1 9603 388 14 8804 0.4 1 8453 351 15 7392 0.4 1 7078 314 16 7581 0.4 1 7281 300 17 6953 0.4 1 6675 278 18 8018 0.4 1 7720 298 19 9923 0.4 1 9604 319 20 10909 0.4 1 10528 381 21 9286 0.4 1 8977 309 22 7933 0.4 1 7632 301 23 8261 0.4 1 7992 269 24 8560 0.4 1 8280 280 25 7971 0.4 1 7711 260 26 7165 0.4 1 6955 210 27 6144 0.4 1 5977 167 28 5350 0.4 1 5202 148 29 5416 0.4 1 5236 180 30 5617 0.4 1 5405 212 31 6416 0.4 1 6216 200 32 7417 0.4 1 7174 243 33 9459 0.4 1 9177 282 34 10556 0.4 1 10233 323 35 10643 0.4 1 10363 280 36 9606 0.4 1 9359 247 37 8213 0.4 1 7974 239 38 6646 0.4 1 6471 175 39 5652 0.4 1 5486 166 40 5728 0.4 1 5534 194 41 6630 0.4 1 6442 188 42 8306 0.4 1 8047 259 43 11184 0.4 1 10893 291 44 13449 0.4 1 13088 361 45 15139 0.4 1 14735 404 46 15324 0.4 1 14880 444 47 13271 0.4 1 12930 341 48 9967 0.4 1 9713 254 49 7766 0.4 1 7541 225 50 6642 0.4 1 6450 192 51 7819 0.4 1 7600 219 52 9814 0.4 1 9550 264 53 13395 0.4 1 13047 348 54 18587 0.4 1 18149 438 55 22093 0.4 1 21580 513 56 23409 0.4 1 22887 522 57 21212 0.4 1 20754 458 58 16669 0.4 1 16319 350 59 11680 0.4 1 11448 232 60 9201 0.4 1 9025 176 61 8791 0.4 1 8612 179 62 11383 0.4 1 11122 261 63 16777 0.4 1 16413 364 64 25592 0.4 1 25138 454 65 31972 0.4 1 31389 583 66 36608 0.4 1 35962 646 67 34983 0.4 1 34404 579 68 28001 0.4 1 27479 522 69 20748 0.4 1 20345 403 70 15129 0.4 1 14775 354 71 11088 0.4 1 10878 210 72 13334 0.4 1 13093 241 73 19614 0.4 1 19274 340 74 32385 0.4 1 31840 545 75 45022 0.4 1 44308 714 76 53554 0.4 1 52683 871 77 57832 0.4 1 56935 897 78 50395 0.4 1 49652 743 79 39594 0.4 1 38858 736 80 28270 0.4 1 27767 503 81 17570 0.4 1 17260 310 82 15975 0.4 1 15657 318 83 20376 0.4 1 20033 343 84 37328 0.4 1 36753 575 85 60210 0.4 1 59240 970 86 83937 0.4 1 82579 1358 87 100160 0.4 1 98662 1498 88 89803 0.4 1 88559 1244 89 72162 0.4 1 71114 1048 90 48607 0.4 1 47900 707 91 30864 0.4 1 30449 415 92 20858 0.4 1 20555 303 93 23053 0.4 1 22756 297 94 41311 0.4 1 40743 568 95 70792 0.4 1 69870 922 96 103051 0.4 1 101789 1262 97 129428 0.4 1 127785 1643 98 129312 0.4 1 127732 1580 99 108573 0.4 1 107261 1312 100 78714 0.4 1 77657 1057 101 49468 0.4 1 48824 644 102 27870 0.4 1 27519 351 103 19695 0.4 1 19389 306 104 29651 0.4 1 29253 398 105 53310 0.4 1 52580 730 106 79665 0.4 1 78725 940 107 93766 0.4 1 92599 1167 108 94863 0.4 1 93776 1087 109 78008 0.4 1 77072 936 110 54969 0.4 1 54243 726 111 33085 0.4 1 32690 395 112 16009 0.4 1 15843 166 113 6719 0.4 1 6618 101 114 5625 0.4 1 5535 90 115 7759 0.4 1 7647 112 116 7994 0.4 1 7879 115 117 8385 0.4 1 8265 120 118 9098 0.4 1 8966 132 119 5513 0.4 1 5418 95 120 2722 0.4 1 2645 77 121 1415 0.4 1 1367 48 122 940 0.4 1 897 43 123 339 0.4 1 268 71 124 162 0.4 1 128 34 125 110 0.4 1 53 57 126 66 0.4 1 31 35 127 74 0.4 1 46 28 128 71 0.4 1 13 58 129 34 0.4 1 10 24 130 36 0.4 1 15 21 131 34 0.4 1 5 29 132 52 0.4 1 20 32 133 87 0.4 1 13 74 134 14 0.4 1 6 8 135 37 0.4 1 4 33 136 22 0.4 1 2 20 137 19 0.4 1 5 14 138 28 0.4 1 4 24 139 27 0.4 1 3 24 140 18 0.4 1 0 18 141 75 0.4 1 9 66 142 40 0.4 1 7 33 143 134 0.4 1 12 122 144 12 0.4 1 4 8 145 17 0.4 1 2 15 146 12 0.4 1 2 10 147 9 0.4 1 3 6 148 63 0.4 1 6 57 149 8 0.4 1 2 6 150 6 0.4 1 1 5 151 361 0.4 1 352 9 RUN STATISTICS FOR INPUT FILE: N1-H-iG-H2A_S8_L002_R2_001.fastq.gz ============================================= 6897700 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 1041 (0.0%)