SUMMARISING RUN PARAMETERS ========================== Input filename: A-N4293-1.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-N4293-1.end2.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 1020.52 s (37 us/read; 1.61 M reads/minute). === Summary === Total reads processed: 27,327,337 Reads with adapters: 10,791,951 (39.5%) Reads written (passing filters): 27,327,337 (100.0%) Total basepairs processed: 1,737,803,865 bp Quality-trimmed: 113,641 bp (0.0%) Total written (filtered): 1,718,673,578 bp (98.9%) === Adapter 1 === Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 10791951 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 27.5% C: 27.0% G: 23.1% T: 22.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 8426801 6831834.2 0 8426801 2 1579378 1707958.6 0 1579378 3 447720 426989.6 0 447720 4 98302 106747.4 0 98302 5 27046 26686.9 0 27046 6 15941 6671.7 0 15941 7 5693 1667.9 0 5693 8 4124 417.0 0 4124 9 4267 104.2 0 3433 834 10 4282 26.1 1 2877 1405 11 4829 6.5 1 3174 1655 12 4220 1.6 1 3285 935 13 4019 1.6 1 3331 688 14 4156 1.6 1 2932 1224 15 3906 1.6 1 2703 1203 16 3237 1.6 1 2577 660 17 3380 1.6 1 2747 633 18 3302 1.6 1 3030 272 19 3950 1.6 1 3516 434 20 4261 1.6 1 3806 455 21 4715 1.6 1 4362 353 22 5743 1.6 1 4744 999 23 6525 1.6 1 6082 443 24 6474 1.6 1 6007 467 25 4983 1.6 1 4626 357 26 4131 1.6 1 3747 384 27 4095 1.6 1 3615 480 28 4662 1.6 1 4211 451 29 5281 1.6 1 4847 434 30 5916 1.6 1 5528 388 31 6571 1.6 1 6114 457 32 7017 1.6 1 6605 412 33 12420 1.6 1 11773 647 34 5742 1.6 1 5307 435 35 9927 1.6 1 9459 468 36 5255 1.6 1 4860 395 37 5165 1.6 1 4831 334 38 8474 1.6 1 8014 460 39 2646 1.6 1 2306 340 40 3694 1.6 1 3375 319 41 1722 1.6 1 1478 244 42 1157 1.6 1 927 230 43 1175 1.6 1 661 514 44 763 1.6 1 520 243 45 955 1.6 1 545 410 46 908 1.6 1 600 308 47 706 1.6 1 484 222 48 1279 1.6 1 876 403 49 1449 1.6 1 1207 242 50 1613 1.6 1 156 1457 51 356 1.6 1 27 329 52 260 1.6 1 12 248 53 510 1.6 1 8 502 54 172 1.6 1 14 158 55 446 1.6 1 6 440 56 220 1.6 1 7 213 57 189 1.6 1 9 180 58 403 1.6 1 5 398 59 271 1.6 1 4 267 60 848 1.6 1 1 847 61 170 1.6 1 1 169 62 251 1.6 1 21 230 63 399 1.6 1 4 395 64 148 1.6 1 5 143 65 170 1.6 1 2 168 66 246 1.6 1 7 239 67 219 1.6 1 2 217 68 428 1.6 1 9 419 69 99 1.6 1 4 95 70 90 1.6 1 4 86 71 65 1.6 1 5 60 72 94 1.6 1 9 85 73 350 1.6 1 15 335 74 138 1.6 1 34 104 75 1344 1.6 1 1166 178 76 88 1.6 1 7 81 RUN STATISTICS FOR INPUT FILE: A-N4293-1.end2.fastq.gz ============================================= 27327337 sequences processed in total TTotal number of sequences analysed for the sequence pair length validation: 27327337 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 22116 (0.08%)