SUMMARISING RUN PARAMETERS ========================== Input filename: N1-M-iG-IgG_S10_L003_R1_001.fastq.gz Trimming mode: single-end Trim Galore version: 0.4.4 Cutadapt version: 1.18 Quality Phred score cutoff: 0 Quality encoding type selected: ASCII+33 Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; user defined) 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 Output file will be GZIP compressed This is cutadapt 1.18 with Python 2.7.13 Command line parameters: -f fastq -e 0.1 -q 0 -O 1 -a CTGTCTCTTATA N1-M-iG-IgG_S10_L003_R1_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 47.14 s (25 us/read; 2.42 M reads/minute). === Summary === Total reads processed: 1,900,828 Reads with adapters: 1,710,438 (90.0%) Reads written (passing filters): 1,900,828 (100.0%) Total basepairs processed: 287,025,028 bp Quality-trimmed: 0 bp (0.0%) Total written (filtered): 153,753,962 bp (53.6%) === Adapter 1 === Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 1710438 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 6.8% C: 48.3% G: 26.5% T: 16.3% none/other: 2.1% Overview of removed sequences length count expect max.err error counts 1 64919 475207.0 0 64919 2 21936 118801.8 0 21936 3 8238 29700.4 0 8238 4 4569 7425.1 0 4569 5 3509 1856.3 0 3509 6 2232 464.1 0 2232 7 2247 116.0 0 2247 8 2331 29.0 0 2331 9 2213 7.3 0 2211 2 10 2586 1.8 1 2374 212 11 2465 0.5 1 2365 100 12 3455 0.1 1 3298 157 13 3753 0.1 1 3592 161 14 4309 0.1 1 4167 142 15 4030 0.1 1 3908 122 16 3301 0.1 1 3170 131 17 3110 0.1 1 3015 95 18 2051 0.1 1 1976 75 19 2963 0.1 1 2855 108 20 2722 0.1 1 2649 73 21 2709 0.1 1 2638 71 22 4405 0.1 1 4269 136 23 4250 0.1 1 4075 175 24 6903 0.1 1 6696 207 25 5299 0.1 1 5154 145 26 5720 0.1 1 5565 155 27 3822 0.1 1 3645 177 28 3002 0.1 1 2913 89 29 2633 0.1 1 2571 62 30 3159 0.1 1 3069 90 31 3167 0.1 1 3074 93 32 4496 0.1 1 4366 130 33 4925 0.1 1 4810 115 34 6960 0.1 1 6754 206 35 7526 0.1 1 7360 166 36 7200 0.1 1 7026 174 37 5636 0.1 1 5454 182 38 4260 0.1 1 4164 96 39 3928 0.1 1 3837 91 40 3154 0.1 1 3032 122 41 3728 0.1 1 3661 67 42 5345 0.1 1 5227 118 43 5926 0.1 1 5801 125 44 7978 0.1 1 7814 164 45 9983 0.1 1 9747 236 46 7973 0.1 1 7827 146 47 7363 0.1 1 7203 160 48 5568 0.1 1 5474 94 49 4609 0.1 1 4463 146 50 3398 0.1 1 3328 70 51 4188 0.1 1 4123 65 52 4732 0.1 1 4638 94 53 6980 0.1 1 6834 146 54 10541 0.1 1 10252 289 55 12781 0.1 1 12567 214 56 13763 0.1 1 13525 238 57 11931 0.1 1 11748 183 58 9522 0.1 1 9324 198 59 7038 0.1 1 6899 139 60 4585 0.1 1 4493 92 61 4434 0.1 1 4359 75 62 5812 0.1 1 5680 132 63 8672 0.1 1 8543 129 64 13524 0.1 1 13295 229 65 17070 0.1 1 16857 213 66 19332 0.1 1 18991 341 67 19737 0.1 1 19391 346 68 16235 0.1 1 15921 314 69 10963 0.1 1 10813 150 70 7656 0.1 1 7533 123 71 5816 0.1 1 5716 100 72 7394 0.1 1 7274 120 73 11999 0.1 1 11757 242 74 17320 0.1 1 16960 360 75 25612 0.1 1 25305 307 76 32126 0.1 1 31617 509 77 32186 0.1 1 31681 505 78 28424 0.1 1 27995 429 79 22857 0.1 1 22546 311 80 14260 0.1 1 14025 235 81 10446 0.1 1 10187 259 82 9309 0.1 1 9079 230 83 13181 0.1 1 13001 180 84 24474 0.1 1 23983 491 85 32103 0.1 1 31718 385 86 44995 0.1 1 44269 726 87 56887 0.1 1 55989 898 88 48419 0.1 1 47723 696 89 38451 0.1 1 37952 499 90 24545 0.1 1 24261 284 91 15810 0.1 1 15531 279 92 11069 0.1 1 10948 121 93 11158 0.1 1 10951 207 94 22168 0.1 1 21858 310 95 35941 0.1 1 35273 668 96 53855 0.1 1 52963 892 97 66384 0.1 1 65378 1006 98 65014 0.1 1 63819 1195 99 51101 0.1 1 50090 1011 100 38015 0.1 1 37421 594 101 22460 0.1 1 22067 393 102 13601 0.1 1 13366 235 103 11405 0.1 1 11215 190 104 15042 0.1 1 14735 307 105 23147 0.1 1 22747 400 106 32941 0.1 1 32408 533 107 41386 0.1 1 40553 833 108 39371 0.1 1 38789 582 109 28350 0.1 1 27834 516 110 20055 0.1 1 19833 222 111 12548 0.1 1 12415 133 112 7322 0.1 1 7187 135 113 3667 0.1 1 3553 114 114 3341 0.1 1 3262 79 115 3407 0.1 1 3361 46 116 2375 0.1 1 2351 24 117 2624 0.1 1 2607 17 118 3601 0.1 1 3557 44 119 1701 0.1 1 1682 19 120 1169 0.1 1 1164 5 121 463 0.1 1 442 21 122 641 0.1 1 635 6 123 90 0.1 1 87 3 124 98 0.1 1 79 19 125 86 0.1 1 85 1 126 59 0.1 1 51 8 127 89 0.1 1 87 2 128 38 0.1 1 31 7 129 1 0.1 1 1 130 15 0.1 1 2 13 131 1 0.1 1 0 1 132 12 0.1 1 12 133 5 0.1 1 1 4 134 38 0.1 1 25 13 136 1 0.1 1 1 137 2 0.1 1 0 2 138 1 0.1 1 0 1 139 1 0.1 1 0 1 141 198 0.1 1 196 2 143 17 0.1 1 0 17 144 5 0.1 1 0 5 145 2 0.1 1 0 2 148 1 0.1 1 1 150 35 0.1 1 35 151 36247 0.1 1 35162 1085 RUN STATISTICS FOR INPUT FILE: N1-M-iG-IgG_S10_L003_R1_001.fastq.gz ============================================= 1900828 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 36565 (1.9%)