SUMMARISING RUN PARAMETERS ========================== Input filename: A-N4293-2.end2.fastq.gz Trimming mode: paired-end Trim Galore version: 0.4.4 Cutadapt version: 1.16 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp All sequences will be trimmed by 1 bp on their 3' end to avoid problems with invalid paired-end alignments with Bowtie 1 Output file will be GZIP compressed This is cutadapt 1.16 with Python 2.7.13 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA A-N4293-2.end2.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 996.11 s (37 us/read; 1.63 M reads/minute). === Summary === Total reads processed: 27,006,792 Reads with adapters: 10,578,684 (39.2%) Reads written (passing filters): 27,006,792 (100.0%) Total basepairs processed: 1,739,309,427 bp Quality-trimmed: 117,540 bp (0.0%) Total written (filtered): 1,721,066,575 bp (99.0%) === Adapter 1 === Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 10578684 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 27.0% C: 27.3% G: 23.3% T: 22.3% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 8233546 6751698.0 0 8233546 2 1584204 1687924.5 0 1584204 3 449657 421981.1 0 449657 4 98885 105495.3 0 98885 5 26543 26373.8 0 26543 6 14575 6593.5 0 14575 7 5181 1648.4 0 5181 8 3686 412.1 0 3686 9 3849 103.0 0 3011 838 10 3902 25.8 1 2452 1450 11 4460 6.4 1 2709 1751 12 3724 1.6 1 2769 955 13 3504 1.6 1 2812 692 14 3695 1.6 1 2430 1265 15 3532 1.6 1 2280 1252 16 3018 1.6 1 2300 718 17 2820 1.6 1 2193 627 18 2947 1.6 1 2660 287 19 3636 1.6 1 3138 498 20 3743 1.6 1 3274 469 21 4062 1.6 1 3730 332 22 5154 1.6 1 4048 1106 23 5510 1.6 1 5113 397 24 5514 1.6 1 5048 466 25 4213 1.6 1 3897 316 26 3647 1.6 1 3273 374 27 3537 1.6 1 3094 443 28 3989 1.6 1 3544 445 29 4507 1.6 1 4131 376 30 5000 1.6 1 4635 365 31 5474 1.6 1 5065 409 32 5890 1.6 1 5467 423 33 10329 1.6 1 9780 549 34 4656 1.6 1 4265 391 35 8318 1.6 1 7847 471 36 4467 1.6 1 4141 326 37 4283 1.6 1 4009 274 38 7088 1.6 1 6637 451 39 2209 1.6 1 1916 293 40 3269 1.6 1 2958 311 41 1606 1.6 1 1324 282 42 1037 1.6 1 827 210 43 1055 1.6 1 547 508 44 672 1.6 1 434 238 45 822 1.6 1 430 392 46 774 1.6 1 483 291 47 652 1.6 1 395 257 48 1088 1.6 1 702 386 49 1189 1.6 1 933 256 50 1629 1.6 1 110 1519 51 369 1.6 1 28 341 52 276 1.6 1 11 265 53 439 1.6 1 6 433 54 157 1.6 1 9 148 55 418 1.6 1 4 414 56 256 1.6 1 5 251 57 208 1.6 1 7 201 58 388 1.6 1 2 386 59 276 1.6 1 1 275 60 929 1.6 1 2 927 61 189 1.6 1 4 185 62 259 1.6 1 26 233 63 398 1.6 1 3 395 64 133 1.6 1 7 126 65 127 1.6 1 1 126 66 193 1.6 1 1 192 67 230 1.6 1 4 226 68 429 1.6 1 5 424 69 79 1.6 1 4 75 70 97 1.6 1 5 92 71 61 1.6 1 1 60 72 116 1.6 1 12 104 73 396 1.6 1 13 383 74 127 1.6 1 27 100 75 1284 1.6 1 1045 239 76 103 1.6 1 6 97 RUN STATISTICS FOR INPUT FILE: A-N4293-2.end2.fastq.gz ============================================= 27006792 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 27006792 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 21440 (0.08%)