SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-135_S35_L005_R2_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-135_S35_L005_R2_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 591.39 s (20 us/read; 2.94 M reads/minute). === Summary === Total reads processed: 28,955,967 Reads with adapters: 18,919,953 (65.3%) Reads written (passing filters): 28,955,967 (100.0%) Total basepairs processed: 2,893,169,841 bp Total written (filtered): 2,564,030,960 bp (88.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 18919953 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 36.5% C: 25.9% G: 9.3% T: 28.2% none/other: 0.1% Overview of removed sequences length count expect max.err error counts 1 9053350 7238991.8 0 9053350 2 231864 1809747.9 0 231864 3 225711 452437.0 0 225711 4 174689 113109.2 0 174689 5 176782 28277.3 0 176782 6 176700 7069.3 0 176700 7 167049 1767.3 0 167049 8 208573 441.8 0 208573 9 165380 110.5 0 164664 716 10 168108 27.6 1 161545 6563 11 161739 6.9 1 152992 8747 12 162479 1.7 1 154421 8058 13 156138 0.4 1 148105 8033 14 175980 0.4 1 167001 8979 15 162266 0.4 1 153913 8353 16 164122 0.4 1 155685 8437 17 173237 0.4 1 164878 8359 18 148379 0.4 1 140722 7657 19 159715 0.4 1 152051 7664 20 159365 0.4 1 150879 8486 21 168324 0.4 1 158379 9945 22 171181 0.4 1 162084 9097 23 157743 0.4 1 149715 8028 24 170040 0.4 1 161255 8785 25 146273 0.4 1 138590 7683 26 156999 0.4 1 147376 9623 27 164517 0.4 1 153138 11379 28 167002 0.4 1 158594 8408 29 165476 0.4 1 154640 10836 30 180602 0.4 1 172027 8575 31 149182 0.4 1 140505 8677 32 157234 0.4 1 150219 7015 33 166525 0.4 1 157127 9398 34 176164 0.4 1 165454 10710 35 159311 0.4 1 152545 6766 36 152144 0.4 1 143498 8646 37 146418 0.4 1 138516 7902 38 135520 0.4 1 128087 7433 39 139186 0.4 1 131155 8031 40 142494 0.4 1 134457 8037 41 137571 0.4 1 131013 6558 42 147024 0.4 1 141093 5931 43 118343 0.4 1 111745 6598 44 131288 0.4 1 124797 6491 45 200349 0.4 1 193357 6992 46 119363 0.4 1 113522 5841 47 80500 0.4 1 75551 4949 48 134178 0.4 1 129005 5173 49 76779 0.4 1 72900 3879 50 88437 0.4 1 83636 4801 51 141647 0.4 1 136849 4798 52 70690 0.4 1 66805 3885 53 79820 0.4 1 75382 4438 54 69979 0.4 1 66089 3890 55 94368 0.4 1 90015 4353 56 91423 0.4 1 86554 4869 57 83357 0.4 1 79108 4249 58 82568 0.4 1 78510 4058 59 77681 0.4 1 73510 4171 60 80292 0.4 1 75938 4354 61 83083 0.4 1 78483 4600 62 91347 0.4 1 86401 4946 63 100064 0.4 1 94848 5216 64 103787 0.4 1 98376 5411 65 107426 0.4 1 102152 5274 66 111384 0.4 1 106044 5340 67 126620 0.4 1 119722 6898 68 254562 0.4 1 247705 6857 69 82726 0.4 1 79073 3653 70 40800 0.4 1 38397 2403 71 26251 0.4 1 24425 1826 72 20937 0.4 1 19377 1560 73 17604 0.4 1 16290 1314 74 15101 0.4 1 13901 1200 75 13184 0.4 1 12079 1105 76 11405 0.4 1 10523 882 77 9867 0.4 1 9116 751 78 8176 0.4 1 7534 642 79 6928 0.4 1 6410 518 80 5117 0.4 1 4689 428 81 3937 0.4 1 3612 325 82 2939 0.4 1 2690 249 83 1986 0.4 1 1837 149 84 1305 0.4 1 1197 108 85 802 0.4 1 743 59 86 567 0.4 1 514 53 87 425 0.4 1 379 46 88 297 0.4 1 256 41 89 264 0.4 1 223 41 90 325 0.4 1 287 38 91 470 0.4 1 395 75 92 691 0.4 1 604 87 93 1430 0.4 1 1261 169 94 3625 0.4 1 3252 373 95 5688 0.4 1 5097 591 96 2958 0.4 1 2676 282 97 1681 0.4 1 1512 169 98 696 0.4 1 615 81 99 626 0.4 1 561 65 100 872 0.4 1 765 107 101 2382 0.4 1 2052 330 RUN STATISTICS FOR INPUT FILE: EPI-135_S35_L005_R2_001.fastq.gz ============================================= 28955967 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 4196008 (14.5%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 18902115 (65.3%) Total number of sequences analysed for the sequence pair length validation: 28955967 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 223177 (0.77%)