SUMMARISING RUN PARAMETERS ========================== Input filename: HMEC_NOMe-Seq-GSM1383850.end1.fastq.gz Trimming mode: paired-end Trim Galore version: 0.4.4 Cutadapt version: 1.16 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp Output file will be GZIP compressed This is cutadapt 1.16 with Python 2.7.13 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC HMEC_NOMe-Seq-GSM1383850.end1.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 8514.03 s (32 us/read; 1.86 M reads/minute). === Summary === Total reads processed: 263,607,668 Reads with adapters: 99,334,034 (37.7%) Reads written (passing filters): 263,607,668 (100.0%) Total basepairs processed: 19,527,098,950 bp Quality-trimmed: 553,934,260 bp (2.8%) Total written (filtered): 18,829,492,591 bp (96.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 99334034 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 38.9% C: 0.6% G: 14.5% T: 45.9% none/other: 0.1% Overview of removed sequences length count expect max.err error counts 1 74546549 65901917.0 0 74546549 2 16851391 16475479.2 0 16851391 3 5507166 4118869.8 0 5507166 4 2144216 1029717.5 0 2144216 5 24757 257429.4 0 24757 6 21080 64357.3 0 21080 7 3266 16089.3 0 3266 8 1446 4022.3 0 1446 9 5470 1005.6 0 1022 4448 10 7598 251.4 1 737 6861 11 3054 62.8 1 685 2369 12 1255 15.7 1 610 645 13 562 3.9 1 489 73 14 986 3.9 1 891 95 15 739 3.9 1 528 211 16 486 3.9 1 403 83 17 711 3.9 1 572 139 18 639 3.9 1 498 141 19 679 3.9 1 561 118 20 1443 3.9 1 1224 219 21 1739 3.9 1 797 942 22 924 3.9 1 764 160 23 22151 3.9 1 20408 1743 24 705 3.9 1 576 129 25 1372 3.9 1 934 438 26 1242 3.9 1 789 453 27 1382 3.9 1 1096 286 28 1102 3.9 1 894 208 29 1355 3.9 1 835 520 30 2798 3.9 1 2191 607 31 20782 3.9 1 19813 969 32 1028 3.9 1 605 423 33 1018 3.9 1 435 583 34 1068 3.9 1 436 632 35 3212 3.9 1 513 2699 36 3828 3.9 1 1721 2107 37 3350 3.9 1 1382 1968 38 1789 3.9 1 801 988 39 468 3.9 1 290 178 40 792 3.9 1 505 287 41 703 3.9 1 158 545 42 1079 3.9 1 285 794 43 989 3.9 1 379 610 44 1194 3.9 1 204 990 45 2184 3.9 1 240 1944 46 1454 3.9 1 483 971 47 1966 3.9 1 228 1738 48 5480 3.9 1 385 5095 49 11320 3.9 1 437 10883 50 45806 3.9 1 327 45479 51 285 3.9 1 86 199 52 491 3.9 1 67 424 53 1077 3.9 1 274 803 54 1310 3.9 1 620 690 55 2106 3.9 1 503 1603 56 2091 3.9 1 1435 656 57 1082 3.9 1 265 817 58 1508 3.9 1 234 1274 59 6981 3.9 1 833 6148 60 9764 3.9 1 5643 4121 61 2573 3.9 1 1375 1198 62 1957 3.9 1 542 1415 63 2756 3.9 1 607 2149 64 5316 3.9 1 1041 4275 65 8316 3.9 1 1721 6595 66 9924 3.9 1 2884 7040 67 4765 3.9 1 2783 1982 68 1733 3.9 1 805 928 69 646 3.9 1 319 327 70 279 3.9 1 175 104 71 109 3.9 1 63 46 72 77 3.9 1 52 25 73 166 3.9 1 138 28 74 28 3.9 1 8 20 75 32 3.9 1 11 21 76 16 3.9 1 6 10 77 19 3.9 1 4 15 78 39 3.9 1 13 26 79 37 3.9 1 22 15 80 37 3.9 1 21 16 81 87 3.9 1 70 17 82 30 3.9 1 0 30 83 19 3.9 1 0 19 84 30 3.9 1 0 30 85 29 3.9 1 0 29 86 30 3.9 1 1 29 87 30 3.9 1 1 29 88 20 3.9 1 0 20 89 27 3.9 1 0 27 90 32 3.9 1 0 32 91 53 3.9 1 0 53 92 31 3.9 1 0 31 93 29 3.9 1 0 29 94 38 3.9 1 0 38 95 26 3.9 1 0 26 96 30 3.9 1 1 29 97 46 3.9 1 0 46 98 37 3.9 1 0 37 99 35 3.9 1 0 35 100 82 3.9 1 0 82 RUN STATISTICS FOR INPUT FILE: HMEC_NOMe-Seq-GSM1383850.end1.fastq.gz ============================================= 263607668 sequences processed in total