SUMMARISING RUN PARAMETERS ========================== Input filename: A-13189-1.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 A-13189-1.end2.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 1177.39 s (36 us/read; 1.65 M reads/minute). === Summary === Total reads processed: 32,315,377 Reads with adapters: 12,762,174 (39.5%) Reads written (passing filters): 32,315,377 (100.0%) Total basepairs processed: 2,054,830,999 bp Quality-trimmed: 81,466 bp (0.0%) Total written (filtered): 2,032,899,711 bp (98.9%) === Adapter 1 === Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 12762174 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 28.3% C: 27.8% G: 22.8% T: 21.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 10120991 8078844.2 0 10120991 2 1834581 2019711.1 0 1834581 3 447533 504927.8 0 447533 4 97699 126231.9 0 97699 5 24496 31558.0 0 24496 6 13448 7889.5 0 13448 7 5426 1972.4 0 5426 8 5033 493.1 0 5033 9 5090 123.3 0 4028 1062 10 4778 30.8 1 3429 1349 11 5978 7.7 1 3801 2177 12 5442 1.9 1 4154 1288 13 5225 1.9 1 4267 958 14 5995 1.9 1 3830 2165 15 5475 1.9 1 3579 1896 16 4147 1.9 1 3125 1022 17 4192 1.9 1 3318 874 18 3796 1.9 1 3475 321 19 4821 1.9 1 4185 636 20 5038 1.9 1 4378 660 21 5525 1.9 1 5129 396 22 7610 1.9 1 6003 1607 23 8318 1.9 1 7854 464 24 8505 1.9 1 7967 538 25 6372 1.9 1 6050 322 26 4905 1.9 1 4521 384 27 4850 1.9 1 4303 547 28 5189 1.9 1 4668 521 29 5825 1.9 1 5370 455 30 6060 1.9 1 5717 343 31 6338 1.9 1 5949 389 32 6891 1.9 1 6487 404 33 12993 1.9 1 12319 674 34 5818 1.9 1 5486 332 35 10338 1.9 1 9950 388 36 5237 1.9 1 4870 367 37 4696 1.9 1 4419 277 38 7860 1.9 1 7417 443 39 2311 1.9 1 2031 280 40 3436 1.9 1 3102 334 41 1544 1.9 1 1307 237 42 1066 1.9 1 901 165 43 1356 1.9 1 580 776 44 657 1.9 1 436 221 45 881 1.9 1 347 534 46 644 1.9 1 334 310 47 493 1.9 1 261 232 48 1029 1.9 1 517 512 49 1096 1.9 1 837 259 50 3129 1.9 1 86 3043 51 509 1.9 1 15 494 52 402 1.9 1 7 395 53 788 1.9 1 2 786 54 143 1.9 1 3 140 55 723 1.9 1 4 719 56 288 1.9 1 3 285 57 238 1.9 1 5 233 58 734 1.9 1 5 729 59 491 1.9 1 5 486 60 2058 1.9 1 1 2057 61 242 1.9 1 2 240 62 348 1.9 1 37 311 63 698 1.9 1 7 691 64 120 1.9 1 8 112 65 171 1.9 1 2 169 66 163 1.9 1 4 159 67 329 1.9 1 7 322 68 526 1.9 1 8 518 69 117 1.9 1 6 111 70 72 1.9 1 3 69 71 46 1.9 1 5 41 72 129 1.9 1 6 123 73 627 1.9 1 19 608 74 172 1.9 1 43 129 75 1818 1.9 1 1515 303 76 66 1.9 1 4 62 RUN STATISTICS FOR INPUT FILE: A-13189-1.end2.fastq.gz ============================================= 32315377 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 32315377 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 27588 (0.09%)