SUMMARISING RUN PARAMETERS ========================== Input filename: Geo_Pool_M_CTTGTA_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 Geo_Pool_M_CTTGTA_L006_R2_001.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 1313.67 s (11 us/read; 5.37 M reads/minute). === Summary === Total reads processed: 117,663,240 Reads with adapters: 35,501,056 (30.2%) Reads written (passing filters): 117,663,240 (100.0%) Total basepairs processed: 11,883,987,240 bp Quality-trimmed: 237,425,663 bp (2.0%) Total written (filtered): 11,577,940,979 bp (97.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 35501056 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 31.4% C: 27.6% G: 21.1% T: 19.9% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 24450304 29415810.0 0 24450304 2 7075603 7353952.5 0 7075603 3 1919893 1838488.1 0 1919893 4 497991 459622.0 0 497991 5 161689 114905.5 0 161689 6 140394 28726.4 0 140394 7 131039 7181.6 0 131039 8 97843 1795.4 0 97843 9 105867 448.8 0 105078 789 10 101622 112.2 1 100317 1305 11 65604 28.1 1 64606 998 12 81956 7.0 1 81028 928 13 54306 1.8 1 53471 835 14 88001 1.8 1 86892 1109 15 26956 1.8 1 26334 622 16 46221 1.8 1 45427 794 17 72447 1.8 1 71198 1249 18 14532 1.8 1 14131 401 19 52653 1.8 1 51900 753 20 21994 1.8 1 21627 367 21 21346 1.8 1 20978 368 22 28174 1.8 1 27647 527 23 24146 1.8 1 23473 673 24 28835 1.8 1 28231 604 25 12030 1.8 1 11754 276 26 17003 1.8 1 16660 343 27 15193 1.8 1 14899 294 28 17107 1.8 1 16893 214 29 8289 1.8 1 8063 226 30 22127 1.8 1 21904 223 31 368 1.8 1 296 72 32 12935 1.8 1 12842 93 33 1642 1.8 1 1588 54 34 6090 1.8 1 6020 70 35 6540 1.8 1 6417 123 36 5260 1.8 1 5191 69 37 5160 1.8 1 5047 113 38 4361 1.8 1 4287 74 39 4410 1.8 1 4308 102 40 3904 1.8 1 3848 56 41 3923 1.8 1 3745 178 42 6239 1.8 1 6117 122 43 661 1.8 1 627 34 44 2682 1.8 1 2593 89 45 4635 1.8 1 4562 73 46 660 1.8 1 623 37 47 1770 1.8 1 1752 18 48 1684 1.8 1 1656 28 49 1691 1.8 1 1661 30 50 1906 1.8 1 1859 47 51 2614 1.8 1 2583 31 52 790 1.8 1 762 28 53 764 1.8 1 748 16 54 1098 1.8 1 1084 14 55 1178 1.8 1 1152 26 56 734 1.8 1 706 28 57 908 1.8 1 884 24 58 1053 1.8 1 1030 23 59 822 1.8 1 796 26 60 904 1.8 1 865 39 61 887 1.8 1 848 39 62 877 1.8 1 791 86 63 1074 1.8 1 950 124 64 1719 1.8 1 1136 583 65 3080 1.8 1 1439 1641 66 2169 1.8 1 1205 964 67 859 1.8 1 564 295 68 309 1.8 1 173 136 69 85 1.8 1 54 31 70 37 1.8 1 24 13 71 42 1.8 1 25 17 72 43 1.8 1 31 12 73 62 1.8 1 31 31 74 81 1.8 1 59 22 75 51 1.8 1 33 18 76 54 1.8 1 27 27 77 55 1.8 1 21 34 78 36 1.8 1 17 19 79 41 1.8 1 14 27 80 32 1.8 1 22 10 81 25 1.8 1 12 13 82 52 1.8 1 8 44 83 82 1.8 1 10 72 84 38 1.8 1 12 26 85 38 1.8 1 6 32 86 29 1.8 1 5 24 87 19 1.8 1 5 14 88 12 1.8 1 4 8 89 20 1.8 1 4 16 90 9 1.8 1 3 6 91 19 1.8 1 2 17 92 13 1.8 1 3 10 93 24 1.8 1 2 22 94 4 1.8 1 1 3 95 4 1.8 1 2 2 96 12 1.8 1 0 12 97 11 1.8 1 0 11 98 27 1.8 1 2 25 99 22 1.8 1 3 19 100 78 1.8 1 0 78 101 374 1.8 1 3 371 RUN STATISTICS FOR INPUT FILE: Geo_Pool_M_CTTGTA_L006_R2_001.fastq ============================================= 117663240 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 918908 (0.8%)