SUMMARISING RUN PARAMETERS ========================== Input filename: KO-N4293-2.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 KO-N4293-2.end2.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 707.49 s (36 us/read; 1.68 M reads/minute). === Summary === Total reads processed: 19,786,147 Reads with adapters: 7,791,002 (39.4%) Reads written (passing filters): 19,786,147 (100.0%) Total basepairs processed: 1,280,554,838 bp Quality-trimmed: 70,605 bp (0.0%) Total written (filtered): 1,267,223,801 bp (99.0%) === Adapter 1 === Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 7791002 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 26.8% C: 27.6% G: 23.6% T: 22.0% none/other: 0.1% Overview of removed sequences length count expect max.err error counts 1 6076652 4946536.8 0 6076652 2 1165803 1236634.2 0 1165803 3 326865 309158.5 0 326865 4 71547 77289.6 0 71547 5 19008 19322.4 0 19008 6 10430 4830.6 0 10430 7 3817 1207.7 0 3817 8 2654 301.9 0 2654 9 2810 75.5 0 2149 661 10 2850 18.9 1 1829 1021 11 3059 4.7 1 1854 1205 12 2784 1.2 1 2062 722 13 2556 1.2 1 2036 520 14 2676 1.2 1 1790 886 15 2558 1.2 1 1711 847 16 1969 1.2 1 1519 450 17 1888 1.2 1 1494 394 18 1996 1.2 1 1759 237 19 2484 1.2 1 2144 340 20 2535 1.2 1 2190 345 21 2797 1.2 1 2536 261 22 3782 1.2 1 3030 752 23 4199 1.2 1 3904 295 24 4058 1.2 1 3744 314 25 2883 1.2 1 2654 229 26 2360 1.2 1 2110 250 27 2317 1.2 1 1968 349 28 2769 1.2 1 2484 285 29 3024 1.2 1 2755 269 30 3469 1.2 1 3245 224 31 3674 1.2 1 3399 275 32 4033 1.2 1 3764 269 33 7329 1.2 1 6930 399 34 3256 1.2 1 3001 255 35 5376 1.2 1 5085 291 36 2835 1.2 1 2577 258 37 2646 1.2 1 2469 177 38 4565 1.2 1 4271 294 39 1476 1.2 1 1262 214 40 2161 1.2 1 1910 251 41 1024 1.2 1 837 187 42 669 1.2 1 519 150 43 772 1.2 1 372 400 44 427 1.2 1 274 153 45 554 1.2 1 255 299 46 458 1.2 1 276 182 47 371 1.2 1 228 143 48 680 1.2 1 396 284 49 730 1.2 1 575 155 50 1219 1.2 1 76 1143 51 275 1.2 1 17 258 52 177 1.2 1 16 161 53 399 1.2 1 5 394 54 126 1.2 1 9 117 55 344 1.2 1 6 338 56 217 1.2 1 3 214 57 162 1.2 1 10 152 58 342 1.2 1 4 338 59 199 1.2 1 1 198 60 818 1.2 1 5 813 61 158 1.2 1 4 154 62 209 1.2 1 54 155 63 346 1.2 1 13 333 64 119 1.2 1 11 108 65 109 1.2 1 2 107 66 161 1.2 1 8 153 67 171 1.2 1 7 164 68 307 1.2 1 7 300 69 66 1.2 1 6 60 70 75 1.2 1 12 63 71 69 1.2 1 12 57 72 87 1.2 1 20 67 73 341 1.2 1 31 310 74 145 1.2 1 54 91 75 2646 1.2 1 2437 209 76 80 1.2 1 17 63 RUN STATISTICS FOR INPUT FILE: KO-N4293-2.end2.fastq.gz ============================================= 19786147 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 19786147 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 18174 (0.09%)