SUMMARISING RUN PARAMETERS ========================== Input filename: smallRNA_100K_R2.fastq.gz Trimming mode: paired-end Trim Galore version: 0.6.4 Cutadapt version: 1.18 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Using smallRNA adapter for trimming (count: 86814). Second best hit was Illumina (count: 0) 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 Output file will be GZIP compressed This is cutadapt 1.18 with Python 3.5.1 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a GATCGTCGGACT smallRNA_100K_R2.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 3.38 s (34 us/read; 1.78 M reads/minute). === Summary === Total reads processed: 100,000 Reads with adapters: 33,193 (33.2%) Reads written (passing filters): 100,000 (100.0%) Total basepairs processed: 5,100,000 bp Quality-trimmed: 9,993 bp (0.2%) Total written (filtered): 5,054,789 bp (99.1%) === Adapter 1 === Sequence: GATCGTCGGACT; Type: regular 3'; Length: 12; Trimmed: 33193 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 75.1% C: 7.0% G: 12.1% T: 5.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 31574 25000.0 0 31574 2 1335 6250.0 0 1335 3 164 1562.5 0 164 4 119 390.6 0 119 6 1 24.4 0 1 RUN STATISTICS FOR INPUT FILE: smallRNA_100K_R2.fastq.gz ============================================= 100000 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 100000 Number of sequence pairs removed because at least one read was shorter than the length cutoff (18 bp): 17169 (17.17%)