SUMMARISING RUN PARAMETERS ========================== Input filename: 4_TGACCA_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 4_TGACCA_L001_R1_001.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 215.97 s (19 us/read; 3.22 M reads/minute). === Summary === Total reads processed: 11,606,618 Reads with adapters: 4,470,755 (38.5%) Reads written (passing filters): 11,606,618 (100.0%) Total basepairs processed: 591,937,518 bp Quality-trimmed: 2,245,132 bp (0.4%) Total written (filtered): 580,602,143 bp (98.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 4470755 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 31.7% C: 1.3% G: 20.3% T: 46.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 3147149 2901654.5 0 3147149 2 722625 725413.6 0 722625 3 250384 181353.4 0 250384 4 108481 45338.4 0 108481 5 21488 11334.6 0 21488 6 18853 2833.6 0 18853 7 16764 708.4 0 16764 8 16269 177.1 0 16269 9 15639 44.3 0 15347 292 10 14359 11.1 1 13593 766 11 13170 2.8 1 12541 629 12 12907 0.7 1 12430 477 13 10766 0.2 1 10328 438 14 11214 0.2 1 10771 443 15 9452 0.2 1 8948 504 16 9996 0.2 1 9523 473 17 8102 0.2 1 7741 361 18 7676 0.2 1 7357 319 19 7168 0.2 1 6807 361 20 6596 0.2 1 6255 341 21 5906 0.2 1 5567 339 22 5435 0.2 1 5122 313 23 4813 0.2 1 4560 253 24 4375 0.2 1 4118 257 25 3610 0.2 1 3432 178 26 2846 0.2 1 2668 178 27 2352 0.2 1 2171 181 28 2192 0.2 1 2045 147 29 1735 0.2 1 1628 107 30 1468 0.2 1 1364 104 31 1005 0.2 1 928 77 32 875 0.2 1 815 60 33 579 0.2 1 549 30 34 335 0.2 1 313 22 35 233 0.2 1 216 17 36 127 0.2 1 119 8 37 91 0.2 1 88 3 38 74 0.2 1 71 3 39 71 0.2 1 66 5 40 71 0.2 1 64 7 41 89 0.2 1 86 3 42 186 0.2 1 170 16 43 201 0.2 1 187 14 44 449 0.2 1 421 28 45 732 0.2 1 699 33 46 739 0.2 1 702 37 47 468 0.2 1 412 56 48 102 0.2 1 95 7 49 41 0.2 1 39 2 50 54 0.2 1 47 7 51 443 0.2 1 360 83 RUN STATISTICS FOR INPUT FILE: 4_TGACCA_L001_R1_001.fastq.gz ============================================= 11606618 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 197762 (1.7%)