SUMMARISING RUN PARAMETERS ========================== Input filename: A-N4293-1.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-N4293-1.end1.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 980.13 s (36 us/read; 1.67 M reads/minute). === Summary === Total reads processed: 27,327,337 Reads with adapters: 10,798,247 (39.5%) Reads written (passing filters): 27,327,337 (100.0%) Total basepairs processed: 1,739,610,724 bp Quality-trimmed: 17,701 bp (0.0%) Total written (filtered): 1,720,463,594 bp (98.9%) === Adapter 1 === Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 10798247 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 27.2% C: 27.2% G: 23.0% T: 22.5% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 8415923 6831834.2 0 8415923 2 1591224 1707958.6 0 1591224 3 451101 426989.6 0 451101 4 99146 106747.4 0 99146 5 26855 26686.9 0 26855 6 16004 6671.7 0 16004 7 5695 1667.9 0 5695 8 4137 417.0 0 4137 9 4235 104.2 0 3399 836 10 4112 26.1 1 2948 1164 11 4728 6.5 1 3255 1473 12 4018 1.6 1 3300 718 13 4058 1.6 1 3403 655 14 4209 1.6 1 3038 1171 15 3785 1.6 1 2711 1074 16 3175 1.6 1 2614 561 17 3375 1.6 1 2847 528 18 3320 1.6 1 3112 208 19 3846 1.6 1 3462 384 20 4390 1.6 1 3968 422 21 4755 1.6 1 4451 304 22 5740 1.6 1 4804 936 23 6385 1.6 1 6066 319 24 6081 1.6 1 5790 291 25 5186 1.6 1 4945 241 26 4196 1.6 1 3944 252 27 4191 1.6 1 3791 400 28 4484 1.6 1 4174 310 29 5437 1.6 1 5072 365 30 6070 1.6 1 5824 246 31 6215 1.6 1 5954 261 32 6918 1.6 1 6657 261 33 8663 1.6 1 8250 413 34 9856 1.6 1 9576 280 35 8317 1.6 1 8066 251 36 6610 1.6 1 6301 309 37 5641 1.6 1 5404 237 38 6421 1.6 1 6059 362 39 5331 1.6 1 5084 247 40 3659 1.6 1 3421 238 41 2085 1.6 1 1847 238 42 1228 1.6 1 1033 195 43 1398 1.6 1 903 495 44 672 1.6 1 448 224 45 823 1.6 1 456 367 46 788 1.6 1 512 276 47 725 1.6 1 524 201 48 1207 1.6 1 820 387 49 1716 1.6 1 1488 228 50 1679 1.6 1 175 1504 51 412 1.6 1 39 373 52 290 1.6 1 13 277 53 545 1.6 1 8 537 54 160 1.6 1 12 148 55 457 1.6 1 8 449 56 236 1.6 1 6 230 57 221 1.6 1 7 214 58 473 1.6 1 2 471 59 240 1.6 1 2 238 60 927 1.6 1 2 925 61 181 1.6 1 5 176 62 224 1.6 1 17 207 63 435 1.6 1 1 434 64 140 1.6 1 7 133 65 165 1.6 1 5 160 66 217 1.6 1 6 211 67 252 1.6 1 7 245 68 461 1.6 1 5 456 69 72 1.6 1 4 68 70 81 1.6 1 1 80 71 44 1.6 1 5 39 72 101 1.6 1 10 91 73 448 1.6 1 9 439 74 155 1.6 1 44 111 75 1440 1.6 1 1249 191 76 57 1.6 1 3 54 RUN STATISTICS FOR INPUT FILE: A-N4293-1.end1.fastq.gz ============================================= 27327337 sequences processed in total