SUMMARISING RUN PARAMETERS ========================== Input filename: 7_CAGATC_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 7_CAGATC_L001_R1_001.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 196.93 s (19 us/read; 3.14 M reads/minute). === Summary === Total reads processed: 10,295,293 Reads with adapters: 4,013,389 (39.0%) Reads written (passing filters): 10,295,293 (100.0%) Total basepairs processed: 525,059,943 bp Quality-trimmed: 1,586,339 bp (0.3%) Total written (filtered): 514,717,887 bp (98.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 4013389 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 31.0% C: 1.5% G: 21.0% T: 46.5% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2753314 2573823.2 0 2753314 2 652174 643455.8 0 652174 3 234852 160864.0 0 234852 4 103251 40216.0 0 103251 5 24247 10054.0 0 24247 6 21578 2513.5 0 21578 7 19539 628.4 0 19539 8 18333 157.1 0 18333 9 18085 39.3 0 17813 272 10 16281 9.8 1 15449 832 11 15275 2.5 1 14558 717 12 14364 0.6 1 13780 584 13 12550 0.2 1 12015 535 14 12626 0.2 1 12023 603 15 11002 0.2 1 10360 642 16 10624 0.2 1 10072 552 17 9315 0.2 1 8892 423 18 8494 0.2 1 8140 354 19 7724 0.2 1 7315 409 20 6985 0.2 1 6624 361 21 6391 0.2 1 6101 290 22 5631 0.2 1 5324 307 23 5161 0.2 1 4876 285 24 4535 0.2 1 4266 269 25 3712 0.2 1 3500 212 26 3101 0.2 1 2926 175 27 2667 0.2 1 2470 197 28 2496 0.2 1 2324 172 29 2116 0.2 1 1986 130 30 1597 0.2 1 1488 109 31 1151 0.2 1 1078 73 32 928 0.2 1 863 65 33 646 0.2 1 616 30 34 388 0.2 1 362 26 35 261 0.2 1 247 14 36 164 0.2 1 147 17 37 73 0.2 1 61 12 38 53 0.2 1 49 4 39 55 0.2 1 50 5 40 49 0.2 1 47 2 41 44 0.2 1 41 3 42 89 0.2 1 82 7 43 89 0.2 1 81 8 44 185 0.2 1 169 16 45 288 0.2 1 271 17 46 364 0.2 1 350 14 47 232 0.2 1 213 19 48 33 0.2 1 28 5 49 15 0.2 1 14 1 50 21 0.2 1 15 6 51 241 0.2 1 199 42 RUN STATISTICS FOR INPUT FILE: 7_CAGATC_L001_R1_001.fastq.gz ============================================= 10295293 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 181439 (1.8%)