SUMMARISING RUN PARAMETERS ========================== Input filename: A-N4371-1.end1.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-N4371-1.end1.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 973.99 s (36 us/read; 1.66 M reads/minute). === Summary === Total reads processed: 26,949,042 Reads with adapters: 10,470,861 (38.9%) Reads written (passing filters): 26,949,042 (100.0%) Total basepairs processed: 1,743,237,637 bp Quality-trimmed: 13,976 bp (0.0%) Total written (filtered): 1,725,826,624 bp (99.0%) === Adapter 1 === Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 10470861 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 27.3% C: 27.5% G: 22.9% T: 22.3% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 8177714 6737260.5 0 8177714 2 1582948 1684315.1 0 1582948 3 426836 421078.8 0 426836 4 95245 105269.7 0 95245 5 24408 26317.4 0 24408 6 13825 6579.4 0 13825 7 4737 1644.8 0 4737 8 3551 411.2 0 3551 9 3490 102.8 0 2664 826 10 3325 25.7 1 2255 1070 11 3936 6.4 1 2484 1452 12 3352 1.6 1 2564 788 13 3226 1.6 1 2512 714 14 3658 1.6 1 2346 1312 15 3267 1.6 1 2096 1171 16 2639 1.6 1 2054 585 17 2706 1.6 1 2120 586 18 2558 1.6 1 2329 229 19 2993 1.6 1 2556 437 20 3398 1.6 1 2953 445 21 3511 1.6 1 3245 266 22 4499 1.6 1 3474 1025 23 4469 1.6 1 4179 290 24 4408 1.6 1 4069 339 25 3718 1.6 1 3527 191 26 3211 1.6 1 2930 281 27 3229 1.6 1 2833 396 28 3368 1.6 1 3042 326 29 3958 1.6 1 3634 324 30 4445 1.6 1 4225 220 31 4483 1.6 1 4226 257 32 4724 1.6 1 4510 214 33 5826 1.6 1 5475 351 34 6335 1.6 1 6105 230 35 5780 1.6 1 5577 203 36 4746 1.6 1 4505 241 37 3719 1.6 1 3515 204 38 4003 1.6 1 3684 319 39 3625 1.6 1 3449 176 40 2544 1.6 1 2303 241 41 1489 1.6 1 1326 163 42 915 1.6 1 745 170 43 1211 1.6 1 617 594 44 492 1.6 1 282 210 45 764 1.6 1 327 437 46 589 1.6 1 336 253 47 530 1.6 1 312 218 48 884 1.6 1 450 434 49 1030 1.6 1 767 263 50 2075 1.6 1 81 1994 51 408 1.6 1 22 386 52 238 1.6 1 10 228 53 631 1.6 1 5 626 54 146 1.6 1 4 142 55 522 1.6 1 3 519 56 258 1.6 1 5 253 57 183 1.6 1 1 182 58 496 1.6 1 5 491 59 318 1.6 1 0 318 60 1243 1.6 1 1 1242 61 181 1.6 1 0 181 62 238 1.6 1 23 215 63 493 1.6 1 2 491 64 130 1.6 1 4 126 65 134 1.6 1 3 131 66 180 1.6 1 4 176 67 224 1.6 1 5 219 68 467 1.6 1 7 460 69 87 1.6 1 2 85 70 86 1.6 1 6 80 71 48 1.6 1 0 48 72 115 1.6 1 13 102 73 515 1.6 1 9 506 74 130 1.6 1 16 114 75 940 1.6 1 710 230 76 58 1.6 1 1 57 RUN STATISTICS FOR INPUT FILE: A-N4371-1.end1.fastq.gz ============================================= 26949042 sequences processed in total