SUMMARISING RUN PARAMETERS ========================== Input filename: /home/sam/Downloads/zr2096/Raw_data/zr2096_10_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_10_s1_R1.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 344.94 s (19 us/read; 3.08 M reads/minute). === Summary === Total reads processed: 17,717,127 Reads with adapters: 8,066,766 (45.5%) Reads written (passing filters): 17,717,127 (100.0%) Total basepairs processed: 1,619,391,518 bp Quality-trimmed: 7,953,221 bp (0.5%) Total written (filtered): 1,596,548,832 bp (98.6%) === Adapter 1 === Sequence: TGGAATTCTCGG; Type: regular 3'; Length: 12; Trimmed: 8066766 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 26.9% C: 6.0% G: 21.7% T: 45.2% none/other: 0.1% Overview of removed sequences length count expect max.err error counts 1 6836099 4429281.8 0 6836099 2 785279 1107320.4 0 785279 3 280553 276830.1 0 280553 4 50900 69207.5 0 50900 5 19406 17301.9 0 19406 6 6096 4325.5 0 6096 7 3109 1081.4 0 3109 8 231 270.3 0 231 9 424 67.6 0 390 34 10 319 16.9 1 160 159 11 279 4.2 1 160 119 12 156 1.1 1 71 85 13 298 1.1 1 157 141 14 152 1.1 1 49 103 15 245 1.1 1 136 109 16 179 1.1 1 109 70 17 230 1.1 1 155 75 18 561 1.1 1 381 180 19 507 1.1 1 378 129 20 136 1.1 1 65 71 21 137 1.1 1 67 70 22 415 1.1 1 272 143 23 452 1.1 1 283 169 24 430 1.1 1 316 114 25 576 1.1 1 414 162 26 538 1.1 1 376 162 27 893 1.1 1 688 205 28 353 1.1 1 240 113 29 464 1.1 1 321 143 30 610 1.1 1 397 213 31 556 1.1 1 388 168 32 820 1.1 1 565 255 33 603 1.1 1 449 154 34 728 1.1 1 555 173 35 741 1.1 1 564 177 36 882 1.1 1 684 198 37 1416 1.1 1 1143 273 38 513 1.1 1 363 150 39 535 1.1 1 379 156 40 590 1.1 1 415 175 41 417 1.1 1 285 132 42 360 1.1 1 255 105 43 639 1.1 1 492 147 44 378 1.1 1 289 89 45 552 1.1 1 415 137 46 974 1.1 1 695 279 47 1020 1.1 1 707 313 48 623 1.1 1 398 225 49 689 1.1 1 509 180 50 675 1.1 1 507 168 51 395 1.1 1 290 105 52 745 1.1 1 569 176 53 945 1.1 1 704 241 54 1060 1.1 1 844 216 55 1798 1.1 1 1454 344 56 1255 1.1 1 990 265 57 878 1.1 1 668 210 58 614 1.1 1 449 165 59 856 1.1 1 668 188 60 1283 1.1 1 1030 253 61 1817 1.1 1 1389 428 62 429 1.1 1 314 115 63 552 1.1 1 432 120 64 1073 1.1 1 826 247 65 1173 1.1 1 884 289 66 1534 1.1 1 1164 370 67 2018 1.1 1 1575 443 68 3376 1.1 1 2743 633 69 1972 1.1 1 1592 380 70 2167 1.1 1 1814 353 71 3104 1.1 1 2698 406 72 4968 1.1 1 4397 571 73 4402 1.1 1 3871 531 74 2816 1.1 1 2417 399 75 1918 1.1 1 1560 358 76 1595 1.1 1 1177 418 77 1719 1.1 1 1226 493 78 1925 1.1 1 1302 623 79 1864 1.1 1 1265 599 80 1778 1.1 1 1246 532 81 1534 1.1 1 1090 444 82 852 1.1 1 582 270 83 513 1.1 1 345 168 84 478 1.1 1 324 154 85 536 1.1 1 347 189 86 545 1.1 1 354 191 87 476 1.1 1 293 183 88 436 1.1 1 284 152 89 404 1.1 1 261 143 90 409 1.1 1 267 142 91 440 1.1 1 283 157 92 414 1.1 1 257 157 93 357 1.1 1 250 107 94 408 1.1 1 262 146 95 365 1.1 1 243 122 96 385 1.1 1 237 148 97 479 1.1 1 307 172 98 462 1.1 1 298 164 99 664 1.1 1 428 236 100 842 1.1 1 560 282 RUN STATISTICS FOR INPUT FILE: /home/sam/Downloads/zr2096/Raw_data/zr2096_10_s1_R1.fastq.gz ============================================= 17717127 sequences processed in total