SUMMARISING RUN PARAMETERS ========================== Input filename: R2.fastq Trimming mode: paired-end Trim Galore version: 0.4.0 Cutadapt version: 1.8.1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; 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 Length cut-off for read 1: 35 bp (default) Length cut-off for read 2: 35 bp (default) This is cutadapt 1.8.1 with Python 2.7.10 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC R2.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 2084.13 s (10 us/read; 5.79 M reads/minute). === Summary === Total reads processed: 200,998,380 Reads with adapters: 72,221,243 (35.9%) Reads written (passing filters): 200,998,380 (100.0%) Total basepairs processed: 15,275,876,880 bp Quality-trimmed: 582,620,358 bp (3.8%) Total written (filtered): 14,547,993,528 bp (95.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 72221243 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 34.2% C: 26.2% G: 17.6% T: 21.1% none/other: 0.9% Overview of removed sequences length count expect max.err error counts 1 53392369 50249595.0 0 53392369 2 12692989 12562398.8 0 12692989 3 3996044 3140599.7 0 3996044 4 898465 785149.9 0 898465 5 199957 196287.5 0 199957 6 41733 49071.9 0 41733 7 21420 12268.0 0 21420 8 16937 3067.0 0 16937 9 21594 766.7 0 15418 6176 10 21338 191.7 1 12772 8566 11 16835 47.9 1 11422 5413 12 12411 12.0 1 11193 1218 13 12316 3.0 1 9998 2318 14 13123 3.0 1 12314 809 15 7466 3.0 1 6846 620 16 8648 3.0 1 7523 1125 17 9515 3.0 1 9033 482 18 5625 3.0 1 5083 542 19 6811 3.0 1 6422 389 20 5214 3.0 1 4965 249 21 4196 3.0 1 3988 208 22 5056 3.0 1 4787 269 23 8323 3.0 1 5755 2568 24 7914 3.0 1 7268 646 25 6468 3.0 1 5960 508 26 10420 3.0 1 5889 4531 27 7100 3.0 1 6000 1100 28 7244 3.0 1 6611 633 29 5672 3.0 1 4854 818 30 12359 3.0 1 11824 535 31 2079 3.0 1 1623 456 32 3282 3.0 1 3072 210 33 2203 3.0 1 2014 189 34 2939 3.0 1 2686 253 35 3399 3.0 1 3149 250 36 3761 3.0 1 3478 283 37 3774 3.0 1 3480 294 38 3903 3.0 1 3569 334 39 4639 3.0 1 4278 361 40 5311 3.0 1 4954 357 41 6074 3.0 1 5422 652 42 11033 3.0 1 10481 552 43 3527 3.0 1 3210 317 44 5255 3.0 1 4529 726 45 7410 3.0 1 6983 427 46 2498 3.0 1 2316 182 47 3537 3.0 1 3265 272 48 2722 3.0 1 2518 204 49 3561 3.0 1 3277 284 50 7011 3.0 1 6634 377 51 5356 3.0 1 5029 327 52 2795 3.0 1 2571 224 53 2345 3.0 1 2117 228 54 4249 3.0 1 4023 226 55 5601 3.0 1 5243 358 56 4440 3.0 1 3896 544 57 5862 3.0 1 5432 430 58 12815 3.0 1 12283 532 59 9503 3.0 1 9079 424 60 11281 3.0 1 10794 487 61 16326 3.0 1 15494 832 62 30462 3.0 1 28919 1543 63 80723 3.0 1 77509 3214 64 147721 3.0 1 137737 9984 65 225595 3.0 1 207184 18411 66 68475 3.0 1 62667 5808 67 10044 3.0 1 8962 1082 68 3200 3.0 1 2861 339 69 1568 3.0 1 1362 206 70 912 3.0 1 808 104 71 836 3.0 1 580 256 72 571 3.0 1 458 113 73 787 3.0 1 415 372 74 613 3.0 1 495 118 75 1057 3.0 1 938 119 76 4626 3.0 1 4181 445 RUN STATISTICS FOR INPUT FILE: R2.fastq ============================================= 200998380 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 200998380 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 5045367 (2.51%)