
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%)
