SUMMARISING RUN PARAMETERS ========================== Input filename: /home/sam/Downloads/zr2096/Raw_data/zr2096_5_s1_R1.fastq.gz Trimming mode: paired-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: 'TGGAATTCTCGG' (Illumina small RNA adapter; auto-detected) Maximum trimming error rate: 0.1 (default) Optional adapter 2 sequence (only used for read 2 of paired-end files): 'GATCGTCGGACT' Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 18 bp All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 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 ~/Downloads/20180411_trimgalore_10bp_Cvirginica_MBD/20180411_fastqc_trim_10bp_Cvirginica_MBD --threads 18 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 TGGAATTCTCGG /home/sam/Downloads/zr2096/Raw_data/zr2096_5_s1_R1.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 582.61 s (18 us/read; 3.27 M reads/minute). === Summary === Total reads processed: 31,778,715 Reads with adapters: 14,444,625 (45.5%) Reads written (passing filters): 31,778,715 (100.0%) Total basepairs processed: 2,881,909,346 bp Quality-trimmed: 9,171,799 bp (0.3%) Total written (filtered): 2,854,903,402 bp (99.1%) === Adapter 1 === Sequence: TGGAATTCTCGG; Type: regular 3'; Length: 12; Trimmed: 14444625 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 27.1% C: 6.0% G: 22.2% T: 44.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 12146141 7944678.8 0 12146141 2 1572510 1986169.7 0 1572510 3 579698 496542.4 0 579698 4 91296 124135.6 0 91296 5 36238 31033.9 0 36238 6 10602 7758.5 0 10602 7 4501 1939.6 0 4501 8 92 484.9 0 92 9 78 121.2 0 15 63 10 162 30.3 1 0 162 11 104 7.6 1 0 104 12 42 1.9 1 0 42 13 62 1.9 1 0 62 14 71 1.9 1 1 70 15 41 1.9 1 0 41 16 40 1.9 1 0 40 17 37 1.9 1 0 37 18 45 1.9 1 0 45 19 28 1.9 1 0 28 20 32 1.9 1 0 32 21 37 1.9 1 0 37 22 48 1.9 1 0 48 23 50 1.9 1 0 50 24 53 1.9 1 0 53 25 40 1.9 1 1 39 26 70 1.9 1 1 69 27 59 1.9 1 0 59 28 34 1.9 1 0 34 29 46 1.9 1 0 46 30 49 1.9 1 0 49 31 38 1.9 1 0 38 32 38 1.9 1 0 38 33 42 1.9 1 0 42 34 44 1.9 1 0 44 35 42 1.9 1 0 42 36 47 1.9 1 0 47 37 37 1.9 1 0 37 38 35 1.9 1 0 35 39 40 1.9 1 0 40 40 41 1.9 1 0 41 41 48 1.9 1 0 48 42 55 1.9 1 0 55 43 49 1.9 1 0 49 44 35 1.9 1 0 35 45 44 1.9 1 0 44 46 43 1.9 1 0 43 47 47 1.9 1 0 47 48 44 1.9 1 0 44 49 46 1.9 1 0 46 50 34 1.9 1 0 34 51 40 1.9 1 0 40 52 58 1.9 1 1 57 53 27 1.9 1 0 27 54 39 1.9 1 0 39 55 37 1.9 1 0 37 56 48 1.9 1 0 48 57 42 1.9 1 0 42 58 36 1.9 1 0 36 59 42 1.9 1 0 42 60 59 1.9 1 1 58 61 45 1.9 1 0 45 62 35 1.9 1 0 35 63 31 1.9 1 0 31 64 32 1.9 1 0 32 65 25 1.9 1 0 25 66 23 1.9 1 0 23 67 35 1.9 1 0 35 68 28 1.9 1 1 27 69 47 1.9 1 0 47 70 27 1.9 1 0 27 71 29 1.9 1 0 29 72 28 1.9 1 0 28 73 22 1.9 1 0 22 74 30 1.9 1 0 30 75 21 1.9 1 0 21 76 20 1.9 1 0 20 77 33 1.9 1 0 33 78 23 1.9 1 0 23 79 35 1.9 1 0 35 80 29 1.9 1 0 29 81 29 1.9 1 0 29 82 32 1.9 1 0 32 83 31 1.9 1 0 31 84 32 1.9 1 0 32 85 27 1.9 1 0 27 86 24 1.9 1 0 24 87 24 1.9 1 0 24 88 29 1.9 1 0 29 89 21 1.9 1 0 21 90 27 1.9 1 0 27 91 25 1.9 1 1 24 92 23 1.9 1 0 23 93 22 1.9 1 0 22 94 22 1.9 1 0 22 95 12 1.9 1 0 12 96 10 1.9 1 0 10 97 15 1.9 1 0 15 98 23 1.9 1 0 23 99 13 1.9 1 0 13 100 3 1.9 1 0 3 RUN STATISTICS FOR INPUT FILE: /home/sam/Downloads/zr2096/Raw_data/zr2096_5_s1_R1.fastq.gz ============================================= 31778715 sequences processed in total