SUMMARISING RUN PARAMETERS ========================== Input filename: /home/sam/Downloads/zr2096/Raw_data/zr2096_6_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_6_s1_R1.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 445.61 s (18 us/read; 3.26 M reads/minute). === Summary === Total reads processed: 24,237,290 Reads with adapters: 10,903,318 (45.0%) Reads written (passing filters): 24,237,290 (100.0%) Total basepairs processed: 2,142,776,317 bp Quality-trimmed: 6,660,811 bp (0.3%) Total written (filtered): 2,122,519,922 bp (99.1%) === Adapter 1 === Sequence: TGGAATTCTCGG; Type: regular 3'; Length: 12; Trimmed: 10903318 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 26.6% C: 6.1% G: 23.4% T: 43.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 9087937 6059322.5 0 9087937 2 1227972 1514830.6 0 1227972 3 467659 378707.7 0 467659 4 75619 94676.9 0 75619 5 30315 23669.2 0 30315 6 7702 5917.3 0 7702 7 3275 1479.3 0 3275 8 61 369.8 0 61 9 59 92.5 0 5 54 10 132 23.1 1 2 130 11 70 5.8 1 0 70 12 47 1.4 1 0 47 13 28 1.4 1 0 28 14 62 1.4 1 0 62 15 27 1.4 1 0 27 16 36 1.4 1 0 36 17 26 1.4 1 0 26 18 45 1.4 1 1 44 19 32 1.4 1 0 32 20 21 1.4 1 0 21 21 44 1.4 1 1 43 22 42 1.4 1 0 42 23 47 1.4 1 0 47 24 28 1.4 1 0 28 25 31 1.4 1 0 31 26 42 1.4 1 0 42 27 31 1.4 1 0 31 28 38 1.4 1 0 38 29 23 1.4 1 0 23 30 43 1.4 1 0 43 31 43 1.4 1 1 42 32 47 1.4 1 0 47 33 36 1.4 1 0 36 34 46 1.4 1 0 46 35 23 1.4 1 0 23 36 30 1.4 1 1 29 37 30 1.4 1 0 30 38 28 1.4 1 0 28 39 33 1.4 1 3 30 40 43 1.4 1 0 43 41 36 1.4 1 0 36 42 57 1.4 1 1 56 43 27 1.4 1 0 27 44 38 1.4 1 0 38 45 33 1.4 1 0 33 46 25 1.4 1 0 25 47 29 1.4 1 0 29 48 53 1.4 1 0 53 49 40 1.4 1 0 40 50 39 1.4 1 0 39 51 27 1.4 1 0 27 52 37 1.4 1 0 37 53 26 1.4 1 0 26 54 30 1.4 1 0 30 55 30 1.4 1 0 30 56 25 1.4 1 0 25 57 30 1.4 1 0 30 58 35 1.4 1 0 35 59 25 1.4 1 0 25 60 30 1.4 1 0 30 61 19 1.4 1 0 19 62 22 1.4 1 0 22 63 24 1.4 1 0 24 64 13 1.4 1 0 13 65 36 1.4 1 0 36 66 23 1.4 1 0 23 67 23 1.4 1 0 23 68 21 1.4 1 0 21 69 33 1.4 1 0 33 70 21 1.4 1 0 21 71 21 1.4 1 0 21 72 27 1.4 1 0 27 73 14 1.4 1 0 14 74 34 1.4 1 0 34 75 21 1.4 1 0 21 76 21 1.4 1 0 21 77 22 1.4 1 0 22 78 22 1.4 1 0 22 79 27 1.4 1 0 27 80 27 1.4 1 0 27 81 21 1.4 1 0 21 82 29 1.4 1 0 29 83 17 1.4 1 0 17 84 25 1.4 1 0 25 85 14 1.4 1 0 14 86 21 1.4 1 0 21 87 18 1.4 1 0 18 88 26 1.4 1 0 26 89 17 1.4 1 0 17 90 15 1.4 1 0 15 91 14 1.4 1 0 14 92 12 1.4 1 0 12 93 15 1.4 1 0 15 94 15 1.4 1 0 15 95 13 1.4 1 0 13 96 11 1.4 1 0 11 97 22 1.4 1 0 22 98 11 1.4 1 0 11 99 5 1.4 1 0 5 100 1 1.4 1 0 1 RUN STATISTICS FOR INPUT FILE: /home/sam/Downloads/zr2096/Raw_data/zr2096_6_s1_R1.fastq.gz ============================================= 24237290 sequences processed in total