SUMMARISING RUN PARAMETERS ========================== Input filename: KO-N4293-1.end2.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: 'CTGTCTCTTATA' (Nextera Transposase sequence; 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 All sequences will be trimmed by 1 bp on their 3' end to avoid problems with invalid paired-end alignments with Bowtie 1 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 CTGTCTCTTATA KO-N4293-1.end2.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 990.69 s (36 us/read; 1.67 M reads/minute). === Summary === Total reads processed: 27,588,151 Reads with adapters: 11,754,885 (42.6%) Reads written (passing filters): 27,588,151 (100.0%) Total basepairs processed: 1,794,155,316 bp Quality-trimmed: 2,704,992 bp (0.2%) Total written (filtered): 1,740,714,253 bp (97.0%) === Adapter 1 === Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 11754885 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 25.2% C: 28.1% G: 23.6% T: 22.5% none/other: 0.6% Overview of removed sequences length count expect max.err error counts 1 8139472 6897037.8 0 8139472 2 1584639 1724259.4 0 1584639 3 476811 431064.9 0 476811 4 119503 107766.2 0 119503 5 47894 26941.6 0 47894 6 29983 6735.4 0 29983 7 23244 1683.8 0 23244 8 21020 421.0 0 21020 9 26475 105.2 0 25624 851 10 29811 26.3 1 21618 8193 11 34377 6.6 1 25178 9199 12 32390 1.6 1 23605 8785 13 32690 1.6 1 24174 8516 14 27155 1.6 1 19885 7270 15 32589 1.6 1 23720 8869 16 23294 1.6 1 17153 6141 17 25308 1.6 1 17594 7714 18 25335 1.6 1 18752 6583 19 35459 1.6 1 24432 11027 20 25501 1.6 1 16822 8679 21 31259 1.6 1 19444 11815 22 37912 1.6 1 18784 19128 23 36924 1.6 1 19222 17702 24 45240 1.6 1 21470 23770 25 45683 1.6 1 19624 26059 26 31791 1.6 1 14229 17562 27 29490 1.6 1 12122 17368 28 35760 1.6 1 15012 20748 29 35844 1.6 1 15695 20149 30 39788 1.6 1 17615 22173 31 53418 1.6 1 24725 28693 32 56915 1.6 1 38015 18900 33 74092 1.6 1 48302 25790 34 34416 1.6 1 22417 11999 35 80749 1.6 1 53293 27456 36 44544 1.6 1 31221 13323 37 37411 1.6 1 25423 11988 38 56067 1.6 1 38735 17332 39 20716 1.6 1 14348 6368 40 37588 1.6 1 26540 11048 41 18233 1.6 1 12624 5609 42 9742 1.6 1 5883 3859 43 7872 1.6 1 4542 3330 44 3868 1.6 1 2406 1462 45 5161 1.6 1 3320 1841 46 4722 1.6 1 3178 1544 47 3540 1.6 1 2279 1261 48 4314 1.6 1 2907 1407 49 5304 1.6 1 3671 1633 50 6914 1.6 1 3837 3077 51 931 1.6 1 404 527 52 584 1.6 1 220 364 53 677 1.6 1 122 555 54 296 1.6 1 97 199 55 582 1.6 1 106 476 56 413 1.6 1 143 270 57 269 1.6 1 65 204 58 530 1.6 1 41 489 59 334 1.6 1 43 291 60 1057 1.6 1 32 1025 61 247 1.6 1 44 203 62 405 1.6 1 126 279 63 787 1.6 1 278 509 64 226 1.6 1 63 163 65 212 1.6 1 70 142 66 270 1.6 1 43 227 67 306 1.6 1 77 229 68 558 1.6 1 59 499 69 187 1.6 1 75 112 70 255 1.6 1 105 150 71 232 1.6 1 111 121 72 329 1.6 1 149 180 73 806 1.6 1 253 553 74 620 1.6 1 383 237 75 3734 1.6 1 3062 672 76 11811 1.6 1 8813 2998 RUN STATISTICS FOR INPUT FILE: KO-N4293-1.end2.fastq.gz ============================================= 27588151 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 27588151 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 45884 (0.17%)