SUMMARISING RUN PARAMETERS ========================== Input filename: 3_TTAGGC_L001_R1_001.fastq.gz Trimming mode: single-end Trim Galore version: 0.4.4_dev 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 10 bp from their 5' end to avoid poor qualities or biases All Read 1 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 /home/sam/analyses/20180503_trimgalore/20180503_trim_fastqc --threads 16 Output file will be GZIP compressed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC 3_TTAGGC_L001_R1_001.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 221.23 s (19 us/read; 3.20 M reads/minute). === Summary === Total reads processed: 11,817,358 Reads with adapters: 4,606,953 (39.0%) Reads written (passing filters): 11,817,358 (100.0%) Total basepairs processed: 602,685,258 bp Quality-trimmed: 2,616,062 bp (0.4%) Total written (filtered): 589,618,988 bp (97.8%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 4606953 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 31.2% C: 1.7% G: 21.0% T: 46.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 3144638 2954339.5 0 3144638 2 749606 738584.9 0 749606 3 263293 184646.2 0 263293 4 117830 46161.6 0 117830 5 28890 11540.4 0 28890 6 25409 2885.1 0 25409 7 22726 721.3 0 22726 8 21766 180.3 0 21766 9 21567 45.1 0 21262 305 10 19726 11.3 1 18729 997 11 18046 2.8 1 17214 832 12 17149 0.7 1 16487 662 13 14709 0.2 1 14113 596 14 15359 0.2 1 14673 686 15 13107 0.2 1 12401 706 16 12953 0.2 1 12295 658 17 11724 0.2 1 11250 474 18 10539 0.2 1 10137 402 19 9528 0.2 1 9077 451 20 9185 0.2 1 8752 433 21 8416 0.2 1 7963 453 22 7405 0.2 1 7045 360 23 6672 0.2 1 6351 321 24 6253 0.2 1 5904 349 25 5200 0.2 1 4911 289 26 4304 0.2 1 4071 233 27 3663 0.2 1 3406 257 28 3422 0.2 1 3191 231 29 2902 0.2 1 2712 190 30 2295 0.2 1 2160 135 31 1760 0.2 1 1652 108 32 1385 0.2 1 1320 65 33 1043 0.2 1 995 48 34 669 0.2 1 641 28 35 389 0.2 1 368 21 36 250 0.2 1 229 21 37 108 0.2 1 101 7 38 87 0.2 1 79 8 39 65 0.2 1 59 6 40 52 0.2 1 49 3 41 64 0.2 1 64 42 127 0.2 1 125 2 43 180 0.2 1 169 11 44 330 0.2 1 313 17 45 541 0.2 1 525 16 46 591 0.2 1 568 23 47 434 0.2 1 382 52 48 87 0.2 1 83 4 49 36 0.2 1 30 6 50 40 0.2 1 33 7 51 433 0.2 1 349 84 RUN STATISTICS FOR INPUT FILE: 3_TTAGGC_L001_R1_001.fastq.gz ============================================= 11817358 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 262037 (2.2%)