SUMMARISING RUN PARAMETERS ========================== Input filename: /Users/sr320/data-genomic/tentacle/OlyOv6/OlyOv6_combined_R1.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) All Read 1 sequences will be trimmed by 14 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 14 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) 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 /Users/sr320/data-genomic/tentacle/OlyOv6/OlyOv6_combined_R1.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 2144.94 s (11 us/read; 5.62 M reads/minute). === Summary === Total reads processed: 200,998,380 Reads with adapters: 73,774,681 (36.7%) Reads written (passing filters): 200,998,380 (100.0%) Total basepairs processed: 15,275,876,880 bp Quality-trimmed: 416,684,162 bp (2.7%) Total written (filtered): 14,564,248,250 bp (95.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 73774681 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 33.0% C: 25.2% G: 17.2% T: 20.3% none/other: 4.3% Overview of removed sequences length count expect max.err error counts 1 52089917 50249595.0 0 52089917 2 13122915 12562398.8 0 13122915 3 3984745 3140599.7 0 3984745 4 876041 785149.9 0 876041 5 192459 196287.5 0 192459 6 42209 49071.9 0 42209 7 21249 12268.0 0 21249 8 16482 3067.0 0 16482 9 17084 766.7 0 12797 4287 10 17718 191.7 1 10499 7219 11 12818 47.9 1 9549 3269 12 12839 12.0 1 11800 1039 13 8626 3.0 1 8184 442 14 8526 3.0 1 8067 459 15 7023 3.0 1 6596 427 16 7179 3.0 1 6596 583 17 7496 3.0 1 6726 770 18 7079 3.0 1 6428 651 19 4954 3.0 1 4399 555 20 5021 3.0 1 4372 649 21 4882 3.0 1 4090 792 22 5126 3.0 1 4458 668 23 6242 3.0 1 4749 1493 24 6742 3.0 1 4742 2000 25 7701 3.0 1 5052 2649 26 7470 3.0 1 4266 3204 27 11441 3.0 1 4746 6695 28 10960 3.0 1 5263 5697 29 12888 3.0 1 5044 7844 30 10274 3.0 1 6240 4034 31 8909 3.0 1 3674 5235 32 9062 3.0 1 4115 4947 33 19175 3.0 1 3926 15249 34 20247 3.0 1 6814 13433 35 20215 3.0 1 6308 13907 36 18977 3.0 1 6897 12080 37 24248 3.0 1 5779 18469 38 29759 3.0 1 7077 22682 39 38372 3.0 1 7309 31063 40 49968 3.0 1 10540 39428 41 34797 3.0 1 13808 20989 42 38698 3.0 1 9281 29417 43 27563 3.0 1 13132 14431 44 38729 3.0 1 6563 32166 45 42853 3.0 1 12030 30823 46 30309 3.0 1 10213 20096 47 27693 3.0 1 7937 19756 48 30221 3.0 1 7209 23012 49 29430 3.0 1 7957 21473 50 28966 3.0 1 7287 21679 51 69734 3.0 1 7286 62448 52 92152 3.0 1 17407 74745 53 41276 3.0 1 19721 21555 54 36134 3.0 1 7428 28706 55 31643 3.0 1 9177 22466 56 48430 3.0 1 7663 40767 57 48431 3.0 1 10921 37510 58 78974 3.0 1 10519 68455 59 52248 3.0 1 17284 34964 60 55257 3.0 1 9701 45556 61 76855 3.0 1 12860 63995 62 175186 3.0 1 17609 157577 63 197887 3.0 1 39008 158879 64 122848 3.0 1 38522 84326 65 85413 3.0 1 22646 62767 66 116361 3.0 1 19925 96436 67 163900 3.0 1 25021 138879 68 271961 3.0 1 37785 234176 69 365011 3.0 1 58318 306693 70 241610 3.0 1 76299 165311 71 145508 3.0 1 38669 106839 72 74901 3.0 1 27598 47303 73 19037 3.0 1 7591 11446 74 13889 3.0 1 4672 9217 75 5707 3.0 1 1628 4079 76 30031 3.0 1 10128 19903 RUN STATISTICS FOR INPUT FILE: /Users/sr320/data-genomic/tentacle/OlyOv6/OlyOv6_combined_R1.fastq ============================================= 200998380 sequences processed in total