SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Pgenr/FASTQS/raw/EPI-167_S10_L002_R1_001.fastq.gz Trimming mode: paired-end Trim Galore version: 0.6.4_dev Cutadapt version: 2.4 Python version: could not detect Number of cores used for trimming: 8 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGCACACGTCTGAAC' (user defined) Maximum trimming error rate: 0.1 (default) Optional adapter 2 sequence (only used for read 2 of paired-end files): 'AGATCGGAAGAGCGTCGTGTAGGGA' 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. Read 1 sequences with adapter contamination will be trimmed a further 2 bp from their 3' end, and Read 2 sequences will be trimmed by 2 bp from their 5' end to remove potential methylation-biased bases from the end-repair reaction All Read 1 sequences will be trimmed by 25 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 25 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: --outdir /gscratch/scrubbed/strigg/analyses/20200316/TG_EPI-Test2 --threads 28 Output file will be GZIP compressed This is cutadapt 2.4 with Python 3.7.6 Command line parameters: -j 8 -e 0.1 -O 1 -a AGATCGGAAGAGCACACGTCTGAAC /gscratch/scrubbed/strigg/analyses/20200316/EPI-167_S10_L002_R1_001.fastq.gz_qual_trimmed.fastq Processing reads on 8 cores in single-end mode ... Finished in 81.72 s (3 us/read; 18.25 M reads/minute). === Summary === Total reads processed: 24,859,230 Reads with adapters: 13,310,825 (53.5%) Reads written (passing filters): 24,859,230 (100.0%) Total basepairs processed: 2,499,293,998 bp Total written (filtered): 2,298,441,331 bp (92.0%) === Adapter 1 === Sequence: AGATCGGAAGAGCACACGTCTGAAC; Type: regular 3'; Length: 25; Trimmed: 13310825 times. No. of allowed errors: 0-9 bp: 0; 10-19 bp: 1; 20-25 bp: 2 Bases preceding removed adapters: A: 25.5% C: 9.5% G: 23.7% T: 41.3% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 5079588 6214807.5 0 5079588 2 1202251 1553701.9 0 1202251 3 456300 388425.5 0 456300 4 315396 97106.4 0 315396 5 162023 24276.6 0 162023 6 154952 6069.1 0 154952 7 141317 1517.3 0 141317 8 147815 379.3 0 147815 9 156397 94.8 0 154875 1522 10 144818 23.7 1 138784 6034 11 151610 5.9 1 144610 7000 12 144234 1.5 1 137849 6385 13 138279 0.4 1 132093 6186 14 149582 0.1 1 141472 8110 15 139617 0.0 1 132371 7246 16 149533 0.0 1 140718 8815 17 143290 0.0 1 134911 8379 18 132507 0.0 1 123777 8159 571 19 143599 0.0 1 132190 10635 774 20 131755 0.0 2 122046 8589 1120 21 146494 0.0 2 132987 11445 2062 22 135126 0.0 2 124303 9630 1193 23 126194 0.0 2 115663 9314 1217 24 131857 0.0 2 119870 10387 1600 25 122353 0.0 2 112116 9190 1047 26 132356 0.0 2 119736 10869 1751 27 119873 0.0 2 109836 8721 1316 28 113147 0.0 2 103784 8301 1062 29 123716 0.0 2 112992 9263 1461 30 113300 0.0 2 103872 8363 1065 31 120517 0.0 2 109240 9537 1740 32 111072 0.0 2 102015 7969 1088 33 114305 0.0 2 104447 8569 1289 34 108779 0.0 2 99492 8120 1167 35 104061 0.0 2 95648 7427 986 36 99353 0.0 2 91169 7175 1009 37 105972 0.0 2 96779 8018 1175 38 92166 0.0 2 84732 6433 1001 39 93699 0.0 2 85639 6965 1095 40 94449 0.0 2 85795 7662 992 41 129224 0.0 2 119820 8107 1297 42 78034 0.0 2 72578 4766 690 43 35611 0.0 2 31892 3292 427 44 72241 0.0 2 66560 4941 740 45 66871 0.0 2 61637 4601 633 46 63480 0.0 2 58567 4379 534 47 65222 0.0 2 59962 4547 713 48 58338 0.0 2 53531 4197 610 49 59861 0.0 2 54840 4380 641 50 53802 0.0 2 49655 3678 469 51 50397 0.0 2 46525 3380 492 52 46801 0.0 2 43097 3252 452 53 42870 0.0 2 39683 2782 405 54 41405 0.0 2 38238 2746 421 55 40756 0.0 2 37782 2611 363 56 36903 0.0 2 34142 2423 338 57 33898 0.0 2 31227 2360 311 58 31239 0.0 2 28980 2027 232 59 30217 0.0 2 28005 1966 246 60 26732 0.0 2 24878 1668 186 61 26427 0.0 2 24460 1787 180 62 25361 0.0 2 23508 1647 206 63 21705 0.0 2 20154 1396 155 64 19937 0.0 2 18653 1152 132 65 17966 0.0 2 16711 1137 118 66 16513 0.0 2 15317 1088 108 67 15408 0.0 2 14252 1052 104 68 14019 0.0 2 12960 970 89 69 13548 0.0 2 12518 939 91 70 12389 0.0 2 11493 818 78 71 12247 0.0 2 11250 892 105 72 14140 0.0 2 12722 1193 225 73 24750 0.0 2 21535 2947 268 74 80751 0.0 2 75790 4690 271 75 62956 0.0 2 59263 3517 176 76 34298 0.0 2 32139 2050 109 77 19980 0.0 2 18745 1172 63 78 11508 0.0 2 10781 686 41 79 6171 0.0 2 5742 410 19 80 3991 0.0 2 3687 279 25 81 2402 0.0 2 2222 166 14 82 1642 0.0 2 1490 140 12 83 1273 0.0 2 1174 88 11 84 1130 0.0 2 1031 91 8 85 989 0.0 2 903 78 8 86 959 0.0 2 877 76 6 87 835 0.0 2 750 78 7 88 716 0.0 2 643 63 10 89 798 0.0 2 727 62 9 90 871 0.0 2 802 64 5 91 1229 0.0 2 1108 109 12 92 1963 0.0 2 1790 160 13 93 4579 0.0 2 4247 306 26 94 13773 0.0 2 12652 1011 110 95 24682 0.0 2 22814 1730 138 96 11975 0.0 2 11015 885 75 97 8863 0.0 2 8123 684 56 98 3854 0.0 2 3544 284 26 99 4127 0.0 2 3800 310 17 100 4411 0.0 2 4002 383 26 101 8135 0.0 2 7184 899 52 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Pgenr/FASTQS/raw/EPI-167_S10_L002_R1_001.fastq.gz ============================================= 24859230 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 2260450 (9.1%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 13261661 (53.3%)