SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-113_S30_L005_R1_001.fastq.gz Trimming mode: paired-end Trim Galore version: 0.4.2 Cutadapt version: 1.12 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 File was specified to be an MspI-digested RRBS sample. Sequences with adapter contamination will be trimmed a further 2 bp to remove potential methylation-biased bases from the end-repair reaction Running FastQC on the data once trimming has completed Output file will be GZIP compressed This is cutadapt 1.12 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -O 1 -a AGATCGGAAGAGC /home/sean/Documents/Geoduck/trimmed-data/EPI-113_S30_L005_R1_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 532.37 s (20 us/read; 2.98 M reads/minute). === Summary === Total reads processed: 26,402,719 Reads with adapters: 14,046,118 (53.2%) Reads written (passing filters): 26,402,719 (100.0%) Total basepairs processed: 2,656,011,145 bp Total written (filtered): 2,443,200,701 bp (92.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 14046118 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 26.4% C: 6.5% G: 25.0% T: 42.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 5543524 6600679.8 0 5543524 2 1285817 1650169.9 0 1285817 3 496423 412542.5 0 496423 4 325074 103135.6 0 325074 5 147119 25783.9 0 147119 6 153049 6446.0 0 153049 7 146963 1611.5 0 146963 8 190999 402.9 0 190999 9 141780 100.7 0 140292 1488 10 139739 25.2 1 133469 6270 11 139353 6.3 1 131997 7356 12 134578 1.6 1 127928 6650 13 123741 0.4 1 117866 5875 14 143057 0.4 1 134706 8351 15 134020 0.4 1 127257 6763 16 139728 0.4 1 131498 8230 17 132030 0.4 1 125018 7012 18 119590 0.4 1 113634 5956 19 133292 0.4 1 125164 8128 20 120685 0.4 1 114757 5928 21 135582 0.4 1 127471 8111 22 126656 0.4 1 120385 6271 23 114488 0.4 1 108405 6083 24 122621 0.4 1 115355 7266 25 110856 0.4 1 105282 5574 26 121902 0.4 1 114888 7014 27 110277 0.4 1 104618 5659 28 104517 0.4 1 99519 4998 29 114607 0.4 1 108573 6034 30 105808 0.4 1 100785 5023 31 113514 0.4 1 106954 6560 32 99616 0.4 1 94879 4737 33 102659 0.4 1 97295 5364 34 97039 0.4 1 92303 4736 35 104824 0.4 1 99054 5770 36 96947 0.4 1 92081 4866 37 103862 0.4 1 98345 5517 38 96642 0.4 1 91926 4716 39 86887 0.4 1 82681 4206 40 99872 0.4 1 94403 5469 41 133769 0.4 1 128163 5606 42 78243 0.4 1 75080 3163 43 37741 0.4 1 35413 2328 44 79833 0.4 1 75969 3864 45 75917 0.4 1 72196 3721 46 75385 0.4 1 71781 3604 47 81761 0.4 1 77508 4253 48 76089 0.4 1 72250 3839 49 75300 0.4 1 71400 3900 50 67442 0.4 1 64399 3043 51 64648 0.4 1 61644 3004 52 61352 0.4 1 58529 2823 53 60190 0.4 1 57633 2557 54 59538 0.4 1 56779 2759 55 61636 0.4 1 58937 2699 56 60018 0.4 1 57351 2667 57 57931 0.4 1 55432 2499 58 54752 0.4 1 52723 2029 59 51705 0.4 1 49658 2047 60 47231 0.4 1 45351 1880 61 48022 0.4 1 46197 1825 62 52962 0.4 1 50988 1974 63 54094 0.4 1 51977 2117 64 55797 0.4 1 53801 1996 65 49777 0.4 1 47963 1814 66 46838 0.4 1 45040 1798 67 40541 0.4 1 38944 1597 68 32627 0.4 1 31429 1198 69 33544 0.4 1 32327 1217 70 29841 0.4 1 28653 1188 71 28251 0.4 1 27173 1078 72 27311 0.4 1 26244 1067 73 31197 0.4 1 29690 1507 74 49407 0.4 1 48119 1288 75 17181 0.4 1 16576 605 76 8532 0.4 1 8236 296 77 5506 0.4 1 5303 203 78 3977 0.4 1 3820 157 79 2662 0.4 1 2547 115 80 1850 0.4 1 1769 81 81 1222 0.4 1 1165 57 82 870 0.4 1 829 41 83 600 0.4 1 572 28 84 343 0.4 1 327 16 85 246 0.4 1 237 9 86 137 0.4 1 128 9 87 106 0.4 1 100 6 88 79 0.4 1 70 9 89 66 0.4 1 55 11 90 76 0.4 1 68 8 91 86 0.4 1 74 12 92 136 0.4 1 124 12 93 179 0.4 1 162 17 94 344 0.4 1 318 26 95 467 0.4 1 437 30 96 423 0.4 1 391 32 97 245 0.4 1 221 24 98 62 0.4 1 55 7 99 45 0.4 1 35 10 100 55 0.4 1 40 15 101 196 0.4 1 121 75 RUN STATISTICS FOR INPUT FILE: EPI-113_S30_L005_R1_001.fastq.gz ============================================= 26402719 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 2776839 (10.5%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 14045160 (53.2%)