SUMMARISING RUN PARAMETERS ========================== Input filename: /home/sam/Downloads/zr2096/Raw_data/zr2096_1_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_1_s1_R1.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 535.85 s (18 us/read; 3.25 M reads/minute). === Summary === Total reads processed: 28,982,766 Reads with adapters: 12,553,900 (43.3%) Reads written (passing filters): 28,982,766 (100.0%) Total basepairs processed: 2,652,423,020 bp Quality-trimmed: 11,158,723 bp (0.4%) Total written (filtered): 2,625,957,959 bp (99.0%) === Adapter 1 === Sequence: TGGAATTCTCGG; Type: regular 3'; Length: 12; Trimmed: 12553900 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 24.8% C: 6.4% G: 22.8% T: 45.9% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 10658399 7245691.5 0 10658399 2 1276010 1811422.9 0 1276010 3 507213 452855.7 0 507213 4 75615 113213.9 0 75615 5 24781 28303.5 0 24781 6 7188 7075.9 0 7188 7 2888 1769.0 0 2888 8 30 442.2 0 30 9 26 110.6 0 7 19 10 90 27.6 1 0 90 11 44 6.9 1 0 44 12 26 1.7 1 0 26 13 24 1.7 1 0 24 14 23 1.7 1 0 23 15 21 1.7 1 0 21 16 22 1.7 1 0 22 17 24 1.7 1 0 24 18 25 1.7 1 0 25 19 18 1.7 1 0 18 20 13 1.7 1 0 13 21 19 1.7 1 0 19 22 19 1.7 1 0 19 23 23 1.7 1 0 23 24 13 1.7 1 0 13 25 22 1.7 1 0 22 26 27 1.7 1 0 27 27 12 1.7 1 0 12 28 24 1.7 1 0 24 29 16 1.7 1 0 16 30 36 1.7 1 0 36 31 18 1.7 1 0 18 32 21 1.7 1 0 21 33 14 1.7 1 0 14 34 24 1.7 1 0 24 35 24 1.7 1 0 24 36 25 1.7 1 0 25 37 23 1.7 1 0 23 38 25 1.7 1 0 25 39 15 1.7 1 0 15 40 19 1.7 1 0 19 41 21 1.7 1 0 21 42 30 1.7 1 0 30 43 20 1.7 1 0 20 44 29 1.7 1 0 29 45 16 1.7 1 0 16 46 24 1.7 1 0 24 47 14 1.7 1 0 14 48 21 1.7 1 0 21 49 23 1.7 1 0 23 50 15 1.7 1 0 15 51 28 1.7 1 0 28 52 16 1.7 1 0 16 53 18 1.7 1 0 18 54 21 1.7 1 0 21 55 19 1.7 1 0 19 56 16 1.7 1 0 16 57 24 1.7 1 0 24 58 13 1.7 1 0 13 59 19 1.7 1 1 18 60 19 1.7 1 0 19 61 18 1.7 1 0 18 62 25 1.7 1 1 24 63 12 1.7 1 0 12 64 18 1.7 1 0 18 65 21 1.7 1 0 21 66 15 1.7 1 0 15 67 24 1.7 1 0 24 68 8 1.7 1 0 8 69 18 1.7 1 0 18 70 19 1.7 1 0 19 71 18 1.7 1 0 18 72 18 1.7 1 0 18 73 23 1.7 1 0 23 74 15 1.7 1 0 15 75 14 1.7 1 0 14 76 12 1.7 1 0 12 77 20 1.7 1 0 20 78 12 1.7 1 0 12 79 15 1.7 1 0 15 80 18 1.7 1 0 18 81 21 1.7 1 0 21 82 15 1.7 1 0 15 83 21 1.7 1 0 21 84 11 1.7 1 0 11 85 11 1.7 1 0 11 86 14 1.7 1 0 14 87 23 1.7 1 0 23 88 15 1.7 1 0 15 89 12 1.7 1 0 12 90 9 1.7 1 0 9 91 12 1.7 1 0 12 92 12 1.7 1 0 12 93 9 1.7 1 0 9 94 11 1.7 1 0 11 95 12 1.7 1 0 12 96 9 1.7 1 0 9 97 13 1.7 1 0 13 98 11 1.7 1 0 11 99 7 1.7 1 0 7 100 4 1.7 1 0 4 RUN STATISTICS FOR INPUT FILE: /home/sam/Downloads/zr2096/Raw_data/zr2096_1_s1_R1.fastq.gz ============================================= 28982766 sequences processed in total