SUMMARISING RUN PARAMETERS ========================== Input filename: MCF7_NOMe-Seq-GSM1383850.end2.fastq.gz Trimming mode: paired-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 for both reads before a sequence pair gets removed: 20 bp 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 MCF7_NOMe-Seq-GSM1383850.end2.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 12584.42 s (48 us/read; 1.25 M reads/minute). === Summary === Total reads processed: 262,903,827 Reads with adapters: 127,075,847 (48.3%) Reads written (passing filters): 262,903,827 (100.0%) Total basepairs processed: 26,290,382,700 bp Quality-trimmed: 1,604,640,410 bp (6.1%) Total written (filtered): 24,557,680,251 bp (93.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 127075847 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 56.6% C: 13.4% G: 0.2% T: 29.7% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 126527849 65725956.8 0 126527849 2 449459 16431489.2 0 449459 3 53974 4107872.3 0 53974 4 23472 1026968.1 0 23472 5 6730 256742.0 0 6730 6 1511 64185.5 0 1511 7 550 16046.4 0 550 8 700 4011.6 0 700 9 1086 1002.9 0 1079 7 10 610 250.7 1 557 53 11 830 62.7 1 743 87 12 552 15.7 1 522 30 13 614 3.9 1 554 60 14 369 3.9 1 338 31 15 357 3.9 1 308 49 16 534 3.9 1 454 80 17 314 3.9 1 265 49 18 349 3.9 1 309 40 19 222 3.9 1 200 22 20 290 3.9 1 267 23 21 328 3.9 1 265 63 22 266 3.9 1 233 33 23 196 3.9 1 172 24 24 126 3.9 1 115 11 25 135 3.9 1 124 11 26 125 3.9 1 99 26 27 241 3.9 1 200 41 28 133 3.9 1 116 17 29 151 3.9 1 124 27 30 139 3.9 1 122 17 31 75 3.9 1 61 14 32 46 3.9 1 41 5 33 47 3.9 1 46 1 34 70 3.9 1 63 7 35 44 3.9 1 40 4 36 44 3.9 1 40 4 37 77 3.9 1 66 11 38 41 3.9 1 39 2 39 96 3.9 1 80 16 40 181 3.9 1 140 41 41 57 3.9 1 48 9 42 35 3.9 1 28 7 43 59 3.9 1 49 10 44 49 3.9 1 42 7 45 40 3.9 1 36 4 46 25 3.9 1 20 5 47 40 3.9 1 34 6 48 26 3.9 1 23 3 49 16 3.9 1 11 5 50 56 3.9 1 49 7 51 29 3.9 1 25 4 52 17 3.9 1 16 1 53 10 3.9 1 8 2 54 27 3.9 1 24 3 55 26 3.9 1 19 7 56 25 3.9 1 17 8 57 45 3.9 1 27 18 58 209 3.9 1 160 49 59 136 3.9 1 108 28 60 71 3.9 1 52 19 61 105 3.9 1 77 28 62 180 3.9 1 119 61 63 470 3.9 1 352 118 64 444 3.9 1 303 141 65 465 3.9 1 304 161 66 187 3.9 1 128 59 67 32 3.9 1 28 4 68 8 3.9 1 5 3 69 6 3.9 1 5 1 70 1 3.9 1 1 71 4 3.9 1 4 72 1 3.9 1 1 73 1 3.9 1 0 1 74 1 3.9 1 1 76 1 3.9 1 0 1 77 1 3.9 1 1 79 1 3.9 1 0 1 81 6 3.9 1 4 2 99 2 3.9 1 0 2 RUN STATISTICS FOR INPUT FILE: MCF7_NOMe-Seq-GSM1383850.end2.fastq.gz ============================================= 262903827 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 262903827 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1646885 (0.63%)