SUMMARISING RUN PARAMETERS ========================== Input filename: Drosophila_melanogaster_BS-Seq-GSM497255.end1.fastq.gz Trimming mode: single-end Trim Galore version: 0.4.4 Cutadapt version: 1.16 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 before a sequence gets removed: 20 bp All Read 1 sequences will be trimmed by 9 bp from their 5' end to avoid poor qualities or biases All Read 1 sequences will be trimmed by 6 bp from their 3' end to avoid poor qualities or biases Output file will be GZIP compressed This is cutadapt 1.16 with Python 2.7.13 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC Drosophila_melanogaster_BS-Seq-GSM497255.end1.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 807.35 s (37 us/read; 1.64 M reads/minute). === Summary === Total reads processed: 22,010,452 Reads with adapters: 10,272,364 (46.7%) Reads written (passing filters): 22,010,452 (100.0%) Total basepairs processed: 1,672,794,352 bp Quality-trimmed: 91,012,453 bp (5.4%) Total written (filtered): 1,474,450,264 bp (88.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 10272364 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 29.7% C: 0.3% G: 22.8% T: 45.7% none/other: 1.5% Overview of removed sequences length count expect max.err error counts 1 2956871 5502613.0 0 2956871 2 1349855 1375653.2 0 1349855 3 570351 343913.3 0 570351 4 333730 85978.3 0 333730 5 210010 21494.6 0 210010 6 289198 5373.6 0 289198 7 237010 1343.4 0 237010 8 219788 335.9 0 219788 9 156240 84.0 0 155157 1083 10 209154 21.0 1 197600 11554 11 171271 5.2 1 161486 9785 12 180336 1.3 1 168903 11433 13 120154 0.3 1 111438 8716 14 238463 0.3 1 219781 18682 15 235406 0.3 1 217353 18053 16 176446 0.3 1 164213 12233 17 172263 0.3 1 160224 12039 18 172556 0.3 1 159733 12823 19 149202 0.3 1 138941 10261 20 131365 0.3 1 122484 8881 21 131089 0.3 1 121535 9554 22 100894 0.3 1 93595 7299 23 155856 0.3 1 144459 11397 24 113370 0.3 1 104475 8895 25 123775 0.3 1 114832 8943 26 120977 0.3 1 112921 8056 27 87784 0.3 1 81928 5856 28 72517 0.3 1 67151 5366 29 110744 0.3 1 102613 8131 30 81666 0.3 1 74913 6753 31 74775 0.3 1 68026 6749 32 97254 0.3 1 89737 7517 33 67614 0.3 1 60910 6704 34 92040 0.3 1 83405 8635 35 94049 0.3 1 83679 10370 36 67230 0.3 1 58303 8927 37 58657 0.3 1 54053 4604 38 31165 0.3 1 28162 3003 39 25976 0.3 1 22785 3191 40 34313 0.3 1 29603 4710 41 31784 0.3 1 25799 5985 42 34045 0.3 1 28080 5965 43 22060 0.3 1 19409 2651 44 11747 0.3 1 9522 2225 45 12974 0.3 1 9961 3013 46 11075 0.3 1 8733 2342 47 8912 0.3 1 5925 2987 48 11640 0.3 1 7515 4125 49 9768 0.3 1 5925 3843 50 4656 0.3 1 3157 1499 51 2904 0.3 1 865 2039 52 4730 0.3 1 1088 3642 53 8553 0.3 1 1296 7257 54 7556 0.3 1 967 6589 55 8774 0.3 1 561 8213 56 6139 0.3 1 691 5448 57 7132 0.3 1 840 6292 58 8733 0.3 1 66 8667 59 12590 0.3 1 75 12515 60 7402 0.3 1 86 7316 61 3215 0.3 1 46 3169 62 2109 0.3 1 166 1943 63 2274 0.3 1 13 2261 64 2354 0.3 1 5 2349 65 2297 0.3 1 4 2293 66 1954 0.3 1 3 1951 67 1431 0.3 1 3 1428 68 941 0.3 1 6 935 69 520 0.3 1 1 519 70 290 0.3 1 2 288 71 105 0.3 1 2 103 72 57 0.3 1 0 57 73 27 0.3 1 0 27 74 23 0.3 1 0 23 75 24 0.3 1 0 24 76 155 0.3 1 0 155 RUN STATISTICS FOR INPUT FILE: Drosophila_melanogaster_BS-Seq-GSM497255.end1.fastq.gz ============================================= 22010452 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 757876 (3.4%)