SUMMARISING RUN PARAMETERS ========================== Input filename: /Users/sr320/data-genomic/tentacle/Geo_Pool_F_GGCTAC_L006_R2_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_R2_001.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 1237.58 s (12 us/read; 5.05 M reads/minute). === Summary === Total reads processed: 104,070,998 Reads with adapters: 36,698,854 (35.3%) Reads written (passing filters): 104,070,998 (100.0%) Total basepairs processed: 10,511,170,798 bp Quality-trimmed: 150,777,819 bp (1.4%) Total written (filtered): 10,286,886,259 bp (97.9%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 36698854 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 34.0% C: 27.6% G: 17.1% T: 21.2% none/other: 0.1% Overview of removed sequences length count expect max.err error counts 1 26153939 26017749.5 0 26153939 2 6228369 6504437.4 0 6228369 3 1938619 1626109.3 0 1938619 4 582435 406527.3 0 582435 5 209124 101631.8 0 209124 6 148620 25408.0 0 148620 7 141477 6352.0 0 141477 8 118367 1588.0 0 118367 9 119274 397.0 0 117193 2081 10 112287 99.2 1 110157 2130 11 79231 24.8 1 77576 1655 12 88909 6.2 1 87742 1167 13 62889 1.6 1 61296 1593 14 88212 1.6 1 87141 1071 15 32297 1.6 1 31572 725 16 50140 1.6 1 49221 919 17 73362 1.6 1 72127 1235 18 18878 1.6 1 18390 488 19 56164 1.6 1 55364 800 20 25818 1.6 1 25377 441 21 25577 1.6 1 25209 368 22 30079 1.6 1 29504 575 23 27440 1.6 1 26515 925 24 31423 1.6 1 30791 632 25 15234 1.6 1 14903 331 26 18175 1.6 1 17626 549 27 16789 1.6 1 16340 449 28 19705 1.6 1 19455 250 29 10913 1.6 1 10351 562 30 29223 1.6 1 28927 296 31 589 1.6 1 419 170 32 16451 1.6 1 16294 157 33 2311 1.6 1 2176 135 34 7978 1.6 1 7814 164 35 8906 1.6 1 8469 437 36 7161 1.6 1 6974 187 37 7135 1.6 1 6704 431 38 5977 1.6 1 5705 272 39 6110 1.6 1 5791 319 40 5684 1.6 1 5569 115 41 6169 1.6 1 5450 719 42 9074 1.6 1 8730 344 43 1019 1.6 1 967 52 44 4070 1.6 1 3829 241 45 6450 1.6 1 6334 116 46 1059 1.6 1 990 69 47 2522 1.6 1 2472 50 48 2376 1.6 1 2324 52 49 2482 1.6 1 2400 82 50 2639 1.6 1 2542 97 51 3781 1.6 1 3720 61 52 1078 1.6 1 1044 34 53 1123 1.6 1 1099 24 54 1612 1.6 1 1566 46 55 1690 1.6 1 1638 52 56 1080 1.6 1 1042 38 57 1340 1.6 1 1252 88 58 1278 1.6 1 1219 59 59 1014 1.6 1 955 59 60 1079 1.6 1 1021 58 61 1137 1.6 1 1038 99 62 1170 1.6 1 955 215 63 1591 1.6 1 1147 444 64 3625 1.6 1 1372 2253 65 7172 1.6 1 1690 5482 66 4560 1.6 1 1414 3146 67 1640 1.6 1 634 1006 68 582 1.6 1 180 402 69 177 1.6 1 76 101 70 124 1.6 1 50 74 71 56 1.6 1 32 24 72 67 1.6 1 33 34 73 114 1.6 1 37 77 74 266 1.6 1 228 38 75 44 1.6 1 27 17 76 66 1.6 1 27 39 77 61 1.6 1 25 36 78 32 1.6 1 17 15 79 52 1.6 1 7 45 80 59 1.6 1 20 39 81 30 1.6 1 12 18 82 36 1.6 1 13 23 83 42 1.6 1 18 24 84 97 1.6 1 8 89 85 57 1.6 1 12 45 86 39 1.6 1 10 29 87 32 1.6 1 5 27 88 23 1.6 1 9 14 89 25 1.6 1 1 24 90 16 1.6 1 6 10 91 65 1.6 1 11 54 92 64 1.6 1 8 56 93 27 1.6 1 4 23 94 16 1.6 1 3 13 95 14 1.6 1 2 12 96 46 1.6 1 3 43 97 16 1.6 1 1 15 98 72 1.6 1 4 68 99 79 1.6 1 2 77 100 230 1.6 1 1 229 101 1027 1.6 1 8 1019 RUN STATISTICS FOR INPUT FILE: /Users/sr320/data-genomic/tentacle/Geo_Pool_F_GGCTAC_L006_R2_001.fastq ============================================= 104070998 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 776217 (0.7%)