SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Pgenr/FASTQS/raw/EPI-167_S10_L002_R2_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 AGATCGGAAGAGCGTCGTGTAGGGA /gscratch/scrubbed/strigg/analyses/20200316/EPI-167_S10_L002_R2_001.fastq.gz_qual_trimmed.fastq Processing reads on 8 cores in single-end mode ... Finished in 85.79 s (3 us/read; 17.39 M reads/minute). === Summary === Total reads processed: 24,859,230 Reads with adapters: 15,363,536 (61.8%) Reads written (passing filters): 24,859,230 (100.0%) Total basepairs processed: 2,488,122,616 bp Total written (filtered): 2,293,251,313 bp (92.2%) === Adapter 1 === Sequence: AGATCGGAAGAGCGTCGTGTAGGGA; Type: regular 3'; Length: 25; Trimmed: 15363536 times. No. of allowed errors: 0-9 bp: 0; 10-19 bp: 1; 20-25 bp: 2 Bases preceding removed adapters: A: 40.3% C: 20.3% G: 7.3% T: 32.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 8554514 6214807.5 0 8554514 2 247131 1553701.9 0 247131 3 191193 388425.5 0 191193 4 164298 97106.4 0 164298 5 160566 24276.6 0 160566 6 159035 6069.1 0 159035 7 150319 1517.3 0 150319 8 152605 379.3 0 152605 9 152922 94.8 0 152285 637 10 151128 23.7 1 146689 4439 11 146920 5.9 1 141612 5308 12 148837 1.5 1 143363 5474 13 142341 0.4 1 137280 5061 14 151875 0.1 1 146116 5759 15 140621 0.0 1 135080 5541 16 140329 0.0 1 134360 5969 17 147590 0.0 1 141058 6532 18 131268 0.0 1 125180 5970 118 19 137242 0.0 1 130202 6888 152 20 134860 0.0 2 126296 7299 1265 21 136470 0.0 2 126594 8307 1569 22 137929 0.0 2 128046 8405 1478 23 132148 0.0 2 122951 7765 1432 24 137535 0.0 2 127293 8713 1529 25 121830 0.0 2 112500 7874 1456 26 122372 0.0 2 111493 9021 1858 27 122833 0.0 2 110779 9719 2335 28 125558 0.0 2 115435 8627 1496 29 121040 0.0 2 109875 9372 1793 30 127761 0.0 2 117798 8505 1458 31 110644 0.0 2 101253 7874 1517 32 113145 0.0 2 104687 7317 1141 33 117931 0.0 2 107886 8506 1539 34 119747 0.0 2 108853 9087 1807 35 109358 0.0 2 101564 6789 1005 36 102469 0.0 2 93985 7185 1299 37 101986 0.0 2 93931 6852 1203 38 88289 0.0 2 81349 5989 951 39 91384 0.0 2 83980 6298 1106 40 87968 0.0 2 81063 5902 1003 41 85810 0.0 2 79585 5436 789 42 82412 0.0 2 76871 4870 671 43 73026 0.0 2 67328 4920 778 44 72521 0.0 2 67133 4755 633 45 84963 0.0 2 79659 4649 655 46 65401 0.0 2 60883 3896 622 47 46340 0.0 2 42573 3316 451 48 62890 0.0 2 58972 3433 485 49 44178 0.0 2 41087 2712 379 50 45926 0.0 2 42356 3132 438 51 59803 0.0 2 56373 3012 418 52 36947 0.0 2 34103 2470 374 53 36693 0.0 2 33991 2310 392 54 32194 0.0 2 29695 2182 317 55 36861 0.0 2 34493 2101 267 56 34269 0.0 2 31729 2174 366 57 30720 0.0 2 28494 1961 265 58 28380 0.0 2 26339 1776 265 59 26631 0.0 2 24733 1671 227 60 25170 0.0 2 23184 1700 286 61 24593 0.0 2 22735 1596 262 62 24060 0.0 2 22223 1561 276 63 22601 0.0 2 20779 1597 225 64 21649 0.0 2 19897 1515 237 65 22204 0.0 2 20390 1572 242 66 24131 0.0 2 22040 1770 321 67 35937 0.0 2 31177 4455 305 68 129003 0.0 2 123606 5023 374 69 47313 0.0 2 44432 2606 275 70 24870 0.0 2 23330 1358 182 71 12976 0.0 2 11952 904 120 72 8650 0.0 2 7938 594 118 73 6006 0.0 2 5428 500 78 74 4673 0.0 2 4170 423 80 75 3587 0.0 2 3246 292 49 76 2967 0.0 2 2644 260 63 77 2595 0.0 2 2287 248 60 78 2277 0.0 2 1988 229 60 79 1974 0.0 2 1740 196 38 80 1588 0.0 2 1403 150 35 81 1399 0.0 2 1220 147 32 82 1178 0.0 2 1020 129 29 83 1067 0.0 2 929 111 27 84 908 0.0 2 767 111 30 85 844 0.0 2 702 108 34 86 765 0.0 2 629 110 26 87 784 0.0 2 659 101 24 88 797 0.0 2 673 96 28 89 913 0.0 2 759 123 31 90 1123 0.0 2 931 153 39 91 1402 0.0 2 1155 188 59 92 2147 0.0 2 1810 255 82 93 4579 0.0 2 3823 597 159 94 13431 0.0 2 11681 1388 362 95 23741 0.0 2 20778 2421 542 96 11598 0.0 2 10136 1204 258 97 8556 0.0 2 7512 866 178 98 3633 0.0 2 3223 345 65 99 3883 0.0 2 3382 409 92 100 4128 0.0 2 3619 404 105 101 7880 0.0 2 6828 858 194 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Pgenr/FASTQS/raw/EPI-167_S10_L002_R2_001.fastq.gz ============================================= 24859230 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 2502338 (10.1%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 0 (0.0%) Total number of sequences analysed for the sequence pair length validation: 24859230 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1422718 (5.72%)