SUMMARISING RUN PARAMETERS ========================== Input filename: KO-13004-1.end1.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: 'CTGTCTCTTATA' (Nextera Transposase sequence; 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 All sequences will be trimmed by 1 bp on their 3' end to avoid problems with invalid paired-end alignments with Bowtie 1 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 CTGTCTCTTATA KO-13004-1.end1.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 1960.56 s (37 us/read; 1.62 M reads/minute). === Summary === Total reads processed: 52,789,893 Reads with adapters: 21,686,958 (41.1%) Reads written (passing filters): 52,789,893 (100.0%) Total basepairs processed: 3,485,178,099 bp Quality-trimmed: 1,383,239 bp (0.0%) Total written (filtered): 3,399,943,156 bp (97.6%) === Adapter 1 === Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 21686958 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 25.3% C: 28.9% G: 23.2% T: 22.3% none/other: 0.3% Overview of removed sequences length count expect max.err error counts 1 15237362 13197473.2 0 15237362 2 3070349 3299368.3 0 3070349 3 864775 824842.1 0 864775 4 219364 206210.5 0 219364 5 81884 51552.6 0 81884 6 49575 12888.2 0 49575 7 38188 3222.0 0 38188 8 34315 805.5 0 34315 9 40273 201.4 0 38547 1726 10 46975 50.3 1 40339 6636 11 49856 12.6 1 40656 9200 12 51796 3.1 1 43981 7815 13 51589 3.1 1 42627 8962 14 51523 3.1 1 43144 8379 15 50370 3.1 1 41079 9291 16 41553 3.1 1 34933 6620 17 42738 3.1 1 35479 7259 18 42540 3.1 1 36333 6207 19 47694 3.1 1 43568 4126 20 54255 3.1 1 48950 5305 21 66855 3.1 1 60906 5949 22 69197 3.1 1 60669 8528 23 72835 3.1 1 64282 8553 24 79584 3.1 1 70905 8679 25 79475 3.1 1 70196 9279 26 66664 3.1 1 58952 7712 27 56139 3.1 1 49351 6788 28 49540 3.1 1 43647 5893 29 60432 3.1 1 53125 7307 30 69632 3.1 1 61591 8041 31 65301 3.1 1 57626 7675 32 66354 3.1 1 59170 7184 33 81451 3.1 1 71323 10128 34 94304 3.1 1 83039 11265 35 100093 3.1 1 90836 9257 36 84169 3.1 1 75810 8359 37 63759 3.1 1 56957 6802 38 50543 3.1 1 44053 6490 39 53633 3.1 1 47207 6426 40 44225 3.1 1 39241 4984 41 30577 3.1 1 26686 3891 42 14656 3.1 1 12873 1783 43 12266 3.1 1 9930 2336 44 3427 3.1 1 2644 783 45 4295 3.1 1 3049 1246 46 3532 3.1 1 2789 743 47 4652 3.1 1 3709 943 48 4748 3.1 1 3550 1198 49 6278 3.1 1 5292 986 50 9700 3.1 1 5648 4052 51 1495 3.1 1 692 803 52 710 3.1 1 175 535 53 1269 3.1 1 114 1155 54 341 3.1 1 55 286 55 1114 3.1 1 48 1066 56 535 3.1 1 43 492 57 401 3.1 1 63 338 58 1043 3.1 1 40 1003 59 616 3.1 1 27 589 60 2590 3.1 1 58 2532 61 456 3.1 1 85 371 62 672 3.1 1 126 546 63 1503 3.1 1 412 1091 64 401 3.1 1 137 264 65 576 3.1 1 264 312 66 738 3.1 1 308 430 67 708 3.1 1 238 470 68 1263 3.1 1 264 999 69 762 3.1 1 521 241 70 579 3.1 1 340 239 71 498 3.1 1 352 146 72 807 3.1 1 552 255 73 2043 3.1 1 994 1049 74 1757 3.1 1 1353 404 75 7235 3.1 1 6372 863 76 21556 3.1 1 19391 2165 RUN STATISTICS FOR INPUT FILE: KO-13004-1.end1.fastq.gz ============================================= 52789893 sequences processed in total