SUMMARISING RUN PARAMETERS ========================== Input filename: A-13190-2.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-13190-2.end2.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 976.65 s (36 us/read; 1.65 M reads/minute). === Summary === Total reads processed: 26,922,264 Reads with adapters: 10,534,376 (39.1%) Reads written (passing filters): 26,922,264 (100.0%) Total basepairs processed: 1,738,150,663 bp Quality-trimmed: 83,688 bp (0.0%) Total written (filtered): 1,720,292,007 bp (99.0%) === Adapter 1 === Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 10534376 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 27.5% C: 27.4% G: 23.2% T: 21.9% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 8239819 6730566.0 0 8239819 2 1575851 1682641.5 0 1575851 3 422522 420660.4 0 422522 4 93803 105165.1 0 93803 5 24131 26291.3 0 24131 6 13158 6572.8 0 13158 7 4904 1643.2 0 4904 8 3856 410.8 0 3856 9 3757 102.7 0 2940 817 10 3951 25.7 1 2516 1435 11 4643 6.4 1 2836 1807 12 3903 1.6 1 2904 999 13 3716 1.6 1 2926 790 14 4121 1.6 1 2663 1458 15 3730 1.6 1 2370 1360 16 2985 1.6 1 2232 753 17 2937 1.6 1 2276 661 18 2870 1.6 1 2614 256 19 3479 1.6 1 2961 518 20 3632 1.6 1 3147 485 21 3980 1.6 1 3606 374 22 5501 1.6 1 4289 1212 23 5825 1.6 1 5443 382 24 5801 1.6 1 5325 476 25 4157 1.6 1 3876 281 26 3414 1.6 1 3070 344 27 3283 1.6 1 2843 440 28 3700 1.6 1 3281 419 29 4284 1.6 1 3857 427 30 4635 1.6 1 4307 328 31 4863 1.6 1 4526 337 32 5333 1.6 1 4969 364 33 9788 1.6 1 9226 562 34 4448 1.6 1 4082 366 35 7386 1.6 1 6962 424 36 3744 1.6 1 3405 339 37 3380 1.6 1 3147 233 38 5719 1.6 1 5245 474 39 1915 1.6 1 1659 256 40 2813 1.6 1 2488 325 41 1388 1.6 1 1133 255 42 958 1.6 1 779 179 43 1105 1.6 1 516 589 44 595 1.6 1 384 211 45 770 1.6 1 335 435 46 602 1.6 1 325 277 47 464 1.6 1 246 218 48 808 1.6 1 472 336 49 889 1.6 1 667 222 50 2005 1.6 1 89 1916 51 419 1.6 1 19 400 52 301 1.6 1 3 298 53 555 1.6 1 1 554 54 136 1.6 1 11 125 55 506 1.6 1 3 503 56 238 1.6 1 3 235 57 162 1.6 1 4 158 58 506 1.6 1 5 501 59 299 1.6 1 3 296 60 1237 1.6 1 2 1235 61 207 1.6 1 3 204 62 275 1.6 1 40 235 63 516 1.6 1 4 512 64 137 1.6 1 5 132 65 141 1.6 1 5 136 66 185 1.6 1 1 184 67 260 1.6 1 2 258 68 474 1.6 1 6 468 69 79 1.6 1 3 76 70 94 1.6 1 7 87 71 58 1.6 1 4 54 72 94 1.6 1 14 80 73 475 1.6 1 14 461 74 136 1.6 1 32 104 75 1468 1.6 1 1234 234 76 97 1.6 1 5 92 RUN STATISTICS FOR INPUT FILE: A-13190-2.end2.fastq.gz ============================================= 26922264 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 26922264 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 22009 (0.08%)