SUMMARISING RUN PARAMETERS ========================== Input filename: KO-13004-1.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: '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.end2.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 1874.42 s (36 us/read; 1.69 M reads/minute). === Summary === Total reads processed: 52,789,893 Reads with adapters: 21,616,442 (40.9%) Reads written (passing filters): 52,789,893 (100.0%) Total basepairs processed: 3,482,393,297 bp Quality-trimmed: 4,166,627 bp (0.1%) Total written (filtered): 3,403,475,799 bp (97.7%) === Adapter 1 === Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 21616442 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 25.6% C: 28.2% G: 23.4% T: 22.3% none/other: 0.5% Overview of removed sequences length count expect max.err error counts 1 15465127 13197473.2 0 15465127 2 3093259 3299368.3 0 3093259 3 880660 824842.1 0 880660 4 219530 206210.5 0 219530 5 79784 51552.6 0 79784 6 47079 12888.2 0 47079 7 35213 3222.0 0 35213 8 31837 805.5 0 31837 9 38907 201.4 0 37274 1633 10 43970 50.3 1 31081 12889 11 50779 12.6 1 36425 14354 12 48562 3.1 1 35006 13556 13 48978 3.1 1 35809 13169 14 40915 3.1 1 29252 11663 15 47726 3.1 1 33862 13864 16 34149 3.1 1 24705 9444 17 35772 3.1 1 24459 11313 18 36470 3.1 1 26697 9773 19 50412 3.1 1 34280 16132 20 36616 3.1 1 24036 12580 21 45054 3.1 1 27935 17119 22 54803 3.1 1 26635 28168 23 52851 3.1 1 27268 25583 24 63666 3.1 1 30307 33359 25 62757 3.1 1 27267 35490 26 44374 3.1 1 19862 24512 27 40490 3.1 1 16429 24061 28 49158 3.1 1 20327 28831 29 48279 3.1 1 20966 27313 30 53603 3.1 1 23612 29991 31 71355 3.1 1 32782 38573 32 75154 3.1 1 49762 25392 33 95588 3.1 1 61555 34033 34 43957 3.1 1 28138 15819 35 100395 3.1 1 65673 34722 36 54875 3.1 1 38193 16682 37 44871 3.1 1 30199 14672 38 63630 3.1 1 43698 19932 39 23209 3.1 1 15968 7241 40 42980 3.1 1 30106 12874 41 20012 3.1 1 13772 6240 42 10386 3.1 1 6128 4258 43 8743 3.1 1 4561 4182 44 4113 3.1 1 2399 1714 45 5266 3.1 1 3098 2168 46 4756 3.1 1 2996 1760 47 3476 3.1 1 2051 1425 48 4035 3.1 1 2365 1670 49 4543 3.1 1 2924 1619 50 7707 3.1 1 2989 4718 51 1236 3.1 1 370 866 52 867 3.1 1 230 637 53 1317 3.1 1 152 1165 54 504 3.1 1 143 361 55 1200 3.1 1 157 1043 56 686 3.1 1 183 503 57 417 3.1 1 66 351 58 1021 3.1 1 59 962 59 639 3.1 1 55 584 60 2433 3.1 1 51 2382 61 476 3.1 1 69 407 62 699 3.1 1 195 504 63 1302 3.1 1 292 1010 64 335 3.1 1 73 262 65 414 3.1 1 92 322 66 492 3.1 1 59 433 67 656 3.1 1 89 567 68 1031 3.1 1 111 920 69 333 3.1 1 129 204 70 443 3.1 1 160 283 71 418 3.1 1 235 183 72 528 3.1 1 234 294 73 1443 3.1 1 419 1024 74 1089 3.1 1 632 457 75 6241 3.1 1 5023 1218 76 20391 3.1 1 15111 5280 RUN STATISTICS FOR INPUT FILE: KO-13004-1.end2.fastq.gz ============================================= 52789893 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 52789893 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 80596 (0.15%)