SUMMARISING RUN PARAMETERS ========================== Input filename: KO-N4293-1.end1.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 KO-N4293-1.end1.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 976.25 s (35 us/read; 1.70 M reads/minute). === Summary === Total reads processed: 27,588,151 Reads with adapters: 11,799,612 (42.8%) Reads written (passing filters): 27,588,151 (100.0%) Total basepairs processed: 1,795,579,096 bp Quality-trimmed: 916,458 bp (0.1%) Total written (filtered): 1,737,179,585 bp (96.7%) === Adapter 1 === Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 11799612 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 24.7% C: 29.0% G: 23.3% T: 22.5% none/other: 0.3% Overview of removed sequences length count expect max.err error counts 1 7969874 6897037.8 0 7969874 2 1565555 1724259.4 0 1565555 3 462483 431064.9 0 462483 4 119228 107766.2 0 119228 5 49276 26941.6 0 49276 6 31755 6735.4 0 31755 7 25433 1683.8 0 25433 8 23173 421.0 0 23173 9 27842 105.2 0 26968 874 10 32264 26.3 1 27864 4400 11 33540 6.6 1 27940 5600 12 34586 1.6 1 29765 4821 13 34647 1.6 1 28934 5713 14 33995 1.6 1 28994 5001 15 34397 1.6 1 28606 5791 16 28586 1.6 1 24422 4164 17 29743 1.6 1 25078 4665 18 29964 1.6 1 25814 4150 19 33530 1.6 1 30988 2542 20 37776 1.6 1 34329 3447 21 45332 1.6 1 41582 3750 22 49124 1.6 1 43713 5411 23 50495 1.6 1 44868 5627 24 57868 1.6 1 51383 6485 25 57476 1.6 1 51140 6336 26 47410 1.6 1 41959 5451 27 40493 1.6 1 35736 4757 28 37545 1.6 1 33222 4323 29 44500 1.6 1 39248 5252 30 52964 1.6 1 46919 6045 31 49583 1.6 1 43711 5872 32 54129 1.6 1 48307 5822 33 54449 1.6 1 48157 6292 34 74041 1.6 1 65445 8596 35 77651 1.6 1 71184 6467 36 74736 1.6 1 67363 7373 37 46570 1.6 1 42155 4415 38 48139 1.6 1 42480 5659 39 39372 1.6 1 35329 4043 40 39629 1.6 1 35539 4090 41 29476 1.6 1 25928 3548 42 13666 1.6 1 12169 1497 43 10098 1.6 1 8680 1418 44 3535 1.6 1 2957 578 45 4405 1.6 1 3521 884 46 3666 1.6 1 3096 570 47 4675 1.6 1 3945 730 48 4922 1.6 1 4050 872 49 7392 1.6 1 6429 963 50 9221 1.6 1 7061 2160 51 1323 1.6 1 874 449 52 459 1.6 1 200 259 53 680 1.6 1 113 567 54 222 1.6 1 67 155 55 550 1.6 1 71 479 56 317 1.6 1 48 269 57 241 1.6 1 77 164 58 455 1.6 1 37 418 59 250 1.6 1 38 212 60 1086 1.6 1 39 1047 61 250 1.6 1 48 202 62 287 1.6 1 89 198 63 813 1.6 1 334 479 64 241 1.6 1 93 148 65 333 1.6 1 178 155 66 370 1.6 1 165 205 67 362 1.6 1 135 227 68 638 1.6 1 157 481 69 406 1.6 1 310 96 70 332 1.6 1 214 118 71 281 1.6 1 192 89 72 481 1.6 1 346 135 73 1019 1.6 1 557 462 74 941 1.6 1 767 174 75 4267 1.6 1 3831 436 76 12799 1.6 1 11599 1200 RUN STATISTICS FOR INPUT FILE: KO-N4293-1.end1.fastq.gz ============================================= 27588151 sequences processed in total