SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/data/coral_RNAseq_2017/porites/4R041-L7-P02-ACAGTG-READ1-Sequences.txt.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: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; 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 Read 1 sequences will be trimmed by 15 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 15 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 4 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 4 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 /mnt/data/coral_RNAseq_2017/porites/20180415_trimmed/fastqc --threads 24 Output file will be GZIP compressed This is cutadapt 1.16 with Python 3.6.4 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /mnt/data/coral_RNAseq_2017/porites/4R041-L7-P02-ACAGTG-READ1-Sequences.txt.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 489.25 s (20 us/read; 2.96 M reads/minute). === Summary === Total reads processed: 24,157,901 Reads with adapters: 9,279,981 (38.4%) Reads written (passing filters): 24,157,901 (100.0%) Total basepairs processed: 2,415,790,100 bp Quality-trimmed: 7,463,230 bp (0.3%) Total written (filtered): 2,371,881,923 bp (98.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 9279981 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 35.9% C: 25.5% G: 17.4% T: 18.9% none/other: 2.3% Overview of removed sequences length count expect max.err error counts 1 6493053 6039475.2 0 6493053 2 1561462 1509868.8 0 1561462 3 492527 377467.2 0 492527 4 132747 94366.8 0 132747 5 47694 23591.7 0 47694 6 26810 5897.9 0 26810 7 22497 1474.5 0 22497 8 20285 368.6 0 20285 9 19122 92.2 0 18630 492 10 21534 23.0 1 16796 4738 11 15785 5.8 1 14653 1132 12 15144 1.4 1 14093 1051 13 13843 0.4 1 12881 962 14 13011 0.4 1 12183 828 15 12750 0.4 1 11919 831 16 11492 0.4 1 10739 753 17 11211 0.4 1 10492 719 18 10757 0.4 1 10076 681 19 9405 0.4 1 8777 628 20 8559 0.4 1 8010 549 21 7561 0.4 1 7070 491 22 6814 0.4 1 6330 484 23 5876 0.4 1 5455 421 24 5443 0.4 1 5128 315 25 4978 0.4 1 4608 370 26 4405 0.4 1 4092 313 27 4318 0.4 1 4014 304 28 4358 0.4 1 4070 288 29 3741 0.4 1 3422 319 30 3699 0.4 1 3427 272 31 3300 0.4 1 3054 246 32 3213 0.4 1 2946 267 33 2874 0.4 1 2600 274 34 2767 0.4 1 2509 258 35 2379 0.4 1 2168 211 36 2332 0.4 1 2161 171 37 2200 0.4 1 2012 188 38 2030 0.4 1 1830 200 39 1678 0.4 1 1525 153 40 1547 0.4 1 1405 142 41 1993 0.4 1 1816 177 42 675 0.4 1 604 71 43 936 0.4 1 847 89 44 769 0.4 1 675 94 45 869 0.4 1 774 95 46 931 0.4 1 852 79 47 921 0.4 1 807 114 48 841 0.4 1 759 82 49 890 0.4 1 792 98 50 837 0.4 1 750 87 51 715 0.4 1 638 77 52 606 0.4 1 513 93 53 740 0.4 1 648 92 54 443 0.4 1 400 43 55 500 0.4 1 439 61 56 397 0.4 1 357 40 57 398 0.4 1 336 62 58 378 0.4 1 331 47 59 341 0.4 1 279 62 60 356 0.4 1 296 60 61 355 0.4 1 317 38 62 304 0.4 1 251 53 63 292 0.4 1 238 54 64 344 0.4 1 280 64 65 339 0.4 1 276 63 66 355 0.4 1 291 64 67 359 0.4 1 287 72 68 345 0.4 1 253 92 69 414 0.4 1 309 105 70 480 0.4 1 283 197 71 682 0.4 1 298 384 72 1471 0.4 1 320 1151 73 22283 0.4 1 369 21914 74 39382 0.4 1 1090 38292 75 31882 0.4 1 1475 30407 76 18907 0.4 1 1069 17838 77 13189 0.4 1 795 12394 78 8690 0.4 1 506 8184 79 5430 0.4 1 362 5068 80 3977 0.4 1 280 3697 81 2710 0.4 1 200 2510 82 1797 0.4 1 151 1646 83 1521 0.4 1 177 1344 84 1129 0.4 1 160 969 85 877 0.4 1 127 750 86 739 0.4 1 125 614 87 602 0.4 1 116 486 88 531 0.4 1 104 427 89 458 0.4 1 71 387 90 443 0.4 1 77 366 91 453 0.4 1 105 348 92 413 0.4 1 58 355 93 475 0.4 1 38 437 94 561 0.4 1 27 534 95 681 0.4 1 46 635 96 917 0.4 1 57 860 97 1283 0.4 1 85 1198 98 1819 0.4 1 53 1766 99 6327 0.4 1 34 6293 100 57028 0.4 1 53 56975 RUN STATISTICS FOR INPUT FILE: /mnt/data/coral_RNAseq_2017/porites/4R041-L7-P02-ACAGTG-READ1-Sequences.txt.gz ============================================= 24157901 sequences processed in total