SUMMARISING RUN PARAMETERS ========================== Input filename: /Users/sr320/data-genomic/tentacle/Geo_Pool_F_GGCTAC_L006_R1_001.fastq Trimming mode: single-end Trim Galore version: 0.4.0 Cutadapt version: 1.8.1 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 before a sequence gets removed: 20 bp Running FastQC on the data once trimming has completed This is cutadapt 1.8.1 with Python 2.7.10 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /Users/sr320/data-genomic/tentacle/Geo_Pool_F_GGCTAC_L006_R1_001.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 1262.64 s (12 us/read; 4.95 M reads/minute). === Summary === Total reads processed: 104,070,998 Reads with adapters: 37,295,736 (35.8%) Reads written (passing filters): 104,070,998 (100.0%) Total basepairs processed: 10,511,170,798 bp Quality-trimmed: 60,385,363 bp (0.6%) Total written (filtered): 10,371,962,798 bp (98.7%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 37295736 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 33.2% C: 27.3% G: 18.0% T: 21.3% none/other: 0.2% Overview of removed sequences length count expect max.err error counts 1 26607903 26017749.5 0 26607903 2 6205626 6504437.4 0 6205626 3 2015304 1626109.3 0 2015304 4 605105 406527.3 0 605105 5 213369 101631.8 0 213369 6 149182 25408.0 0 149182 7 135972 6352.0 0 135972 8 121962 1588.0 0 121962 9 119594 397.0 0 117688 1906 10 105176 99.2 1 102213 2963 11 88007 24.8 1 85816 2191 12 85821 6.2 1 83926 1895 13 67361 1.6 1 65457 1904 14 62670 1.6 1 61353 1317 15 54158 1.6 1 52922 1236 16 52418 1.6 1 50649 1769 17 45872 1.6 1 44547 1325 18 53653 1.6 1 51881 1772 19 32783 1.6 1 31807 976 20 38147 1.6 1 36991 1156 21 33876 1.6 1 32792 1084 22 29957 1.6 1 29027 930 23 26946 1.6 1 25903 1043 24 24287 1.6 1 23345 942 25 20639 1.6 1 19936 703 26 17259 1.6 1 16587 672 27 16749 1.6 1 16162 587 28 16867 1.6 1 16228 639 29 15343 1.6 1 14818 525 30 15312 1.6 1 14839 473 31 11469 1.6 1 11036 433 32 11638 1.6 1 11297 341 33 9508 1.6 1 9202 306 34 9567 1.6 1 9247 320 35 8649 1.6 1 8336 313 36 7529 1.6 1 7227 302 37 7203 1.6 1 6931 272 38 6549 1.6 1 6284 265 39 5949 1.6 1 5672 277 40 6630 1.6 1 6219 411 41 7612 1.6 1 7372 240 42 3156 1.6 1 2969 187 43 4344 1.6 1 4203 141 44 3313 1.6 1 2980 333 45 4063 1.6 1 3670 393 46 3833 1.6 1 3560 273 47 2700 1.6 1 2496 204 48 2610 1.6 1 2426 184 49 2761 1.6 1 2577 184 50 2249 1.6 1 2072 177 51 2525 1.6 1 2172 353 52 2566 1.6 1 2157 409 53 2534 1.6 1 2364 170 54 1290 1.6 1 1091 199 55 1618 1.6 1 1328 290 56 1541 1.6 1 1287 254 57 1607 1.6 1 1360 247 58 1465 1.6 1 1005 460 59 1456 1.6 1 1271 185 60 1376 1.6 1 671 705 61 1132 1.6 1 867 265 62 1482 1.6 1 748 734 63 2263 1.6 1 993 1270 64 1402 1.6 1 752 650 65 1083 1.6 1 436 647 66 1426 1.6 1 509 917 67 2172 1.6 1 580 1592 68 3517 1.6 1 595 2922 69 13060 1.6 1 594 12466 70 12407 1.6 1 1062 11345 71 10499 1.6 1 732 9767 72 6011 1.6 1 498 5513 73 4624 1.6 1 266 4358 74 3658 1.6 1 232 3426 75 909 1.6 1 85 824 76 757 1.6 1 40 717 77 654 1.6 1 19 635 78 449 1.6 1 12 437 79 324 1.6 1 13 311 80 236 1.6 1 11 225 81 160 1.6 1 13 147 82 139 1.6 1 10 129 83 117 1.6 1 21 96 84 115 1.6 1 8 107 85 77 1.6 1 17 60 86 66 1.6 1 17 49 87 59 1.6 1 6 53 88 50 1.6 1 11 39 89 51 1.6 1 6 45 90 41 1.6 1 9 32 91 123 1.6 1 15 108 92 87 1.6 1 7 80 93 70 1.6 1 3 67 94 101 1.6 1 1 100 95 118 1.6 1 3 115 96 352 1.6 1 7 345 97 271 1.6 1 3 268 98 402 1.6 1 3 399 99 679 1.6 1 3 676 100 1933 1.6 1 4 1929 101 6032 1.6 1 14 6018 RUN STATISTICS FOR INPUT FILE: /Users/sr320/data-genomic/tentacle/Geo_Pool_F_GGCTAC_L006_R1_001.fastq ============================================= 104070998 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 159359 (0.2%)