SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-128_S34_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-128_S34_L005_R1_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 492.61 s (20 us/read; 3.01 M reads/minute). === Summary === Total reads processed: 24,692,504 Reads with adapters: 12,882,369 (52.2%) Reads written (passing filters): 24,692,504 (100.0%) Total basepairs processed: 2,483,847,019 bp Total written (filtered): 2,292,350,949 bp (92.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 12882369 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 26.8% C: 6.6% G: 23.7% T: 42.9% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 5316394 6173126.0 0 5316394 2 1204822 1543281.5 0 1204822 3 461612 385820.4 0 461612 4 298071 96455.1 0 298071 5 127215 24113.8 0 127215 6 130586 6028.4 0 130586 7 122418 1507.1 0 122418 8 158353 376.8 0 158353 9 121484 94.2 0 120254 1230 10 118715 23.5 1 111966 6749 11 118974 5.9 1 111241 7733 12 113993 1.5 1 107006 6987 13 106012 0.4 1 99441 6571 14 121314 0.4 1 112716 8598 15 114798 0.4 1 107351 7447 16 122344 0.4 1 113401 8943 17 112284 0.4 1 104954 7330 18 102317 0.4 1 95760 6557 19 113237 0.4 1 105114 8123 20 104113 0.4 1 97563 6550 21 117077 0.4 1 108439 8638 22 109218 0.4 1 102392 6826 23 97365 0.4 1 90688 6677 24 104186 0.4 1 96796 7390 25 93103 0.4 1 87188 5915 26 106270 0.4 1 98581 7689 27 93274 0.4 1 87503 5771 28 88566 0.4 1 82997 5569 29 98825 0.4 1 92307 6518 30 91339 0.4 1 85675 5664 31 96577 0.4 1 89891 6686 32 88217 0.4 1 82799 5418 33 91068 0.4 1 85113 5955 34 82686 0.4 1 77714 4972 35 84016 0.4 1 78860 5156 36 82127 0.4 1 76939 5188 37 90217 0.4 1 84260 5957 38 86828 0.4 1 80921 5907 39 78598 0.4 1 73652 4946 40 81960 0.4 1 76071 5889 41 114324 0.4 1 107811 6513 42 70536 0.4 1 66792 3744 43 35346 0.4 1 32506 2840 44 70287 0.4 1 65796 4491 45 67741 0.4 1 63640 4101 46 67535 0.4 1 63427 4108 47 72894 0.4 1 68050 4844 48 69320 0.4 1 64740 4580 49 67099 0.4 1 62676 4423 50 60547 0.4 1 56858 3689 51 57322 0.4 1 53915 3407 52 54441 0.4 1 51137 3304 53 53839 0.4 1 50732 3107 54 54017 0.4 1 50802 3215 55 56653 0.4 1 53501 3152 56 53858 0.4 1 50663 3195 57 52880 0.4 1 49945 2935 58 48851 0.4 1 46292 2559 59 47065 0.4 1 44562 2503 60 43515 0.4 1 41245 2270 61 44456 0.4 1 42279 2177 62 48289 0.4 1 45801 2488 63 50286 0.4 1 47699 2587 64 51756 0.4 1 49233 2523 65 46910 0.4 1 44570 2340 66 44395 0.4 1 42155 2240 67 38494 0.4 1 36614 1880 68 31379 0.4 1 29797 1582 69 32441 0.4 1 30753 1688 70 29644 0.4 1 28135 1509 71 28994 0.4 1 27484 1510 72 27667 0.4 1 26081 1586 73 30048 0.4 1 28098 1950 74 48077 0.4 1 46214 1863 75 21216 0.4 1 20185 1031 76 11652 0.4 1 11071 581 77 7453 0.4 1 7090 363 78 5216 0.4 1 4959 257 79 3435 0.4 1 3247 188 80 2308 0.4 1 2182 126 81 1520 0.4 1 1435 85 82 1046 0.4 1 985 61 83 705 0.4 1 654 51 84 454 0.4 1 428 26 85 276 0.4 1 258 18 86 206 0.4 1 197 9 87 107 0.4 1 102 5 88 101 0.4 1 93 8 89 70 0.4 1 61 9 90 117 0.4 1 102 15 91 131 0.4 1 117 14 92 241 0.4 1 220 21 93 399 0.4 1 364 35 94 960 0.4 1 895 65 95 1407 0.4 1 1315 92 96 816 0.4 1 754 62 97 380 0.4 1 346 34 98 126 0.4 1 111 15 99 93 0.4 1 81 12 100 141 0.4 1 117 24 101 314 0.4 1 209 105 RUN STATISTICS FOR INPUT FILE: EPI-128_S34_L005_R1_001.fastq.gz ============================================= 24692504 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 2573906 (10.4%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 12880581 (52.2%)