SUMMARISING RUN PARAMETERS
==========================
Input filename: Samples/H3K4me3_Liver_A/raw_reads.fq.gz
Trimming mode: single-end
Trim Galore version: 0.4.0
Cutadapt version: 1.12
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 before a sequence gets removed: 20 bp
Output file will be GZIP compressed


This is cutadapt 1.12 with Python 2.7.6
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC Samples/H3K4me3_Liver_A/raw_reads.fq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 457.37 s (27 us/read; 2.25 M reads/minute).

=== Summary ===

Total reads processed:              17,143,420
Reads with adapters:                 5,846,106 (34.1%)
Reads written (passing filters):    17,143,420 (100.0%)

Total basepairs processed:   874,314,420 bp
Quality-trimmed:                 634,758 bp (0.1%)
Total written (filtered):    865,110,481 bp (98.9%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 5846106 times.

No. of allowed errors:
0-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 32.9%
  C: 30.4%
  G: 18.2%
  T: 18.3%
  none/other: 0.2%

Overview of removed sequences
length	count	expect	max.err	error counts
1	4210797	4285855.0	0	4210797
2	1193618	1071463.8	0	1193618
3	342436	267865.9	0	342436
4	69571	66966.5	0	69571
5	13276	16741.6	0	13276
6	1028	4185.4	0	1028
7	479	1046.4	0	479
8	252	261.6	0	252
9	380	65.4	0	190 190
10	544	16.3	1	211 333
11	320	4.1	1	160 160
12	218	1.0	1	142 76
13	234	0.3	1	171 63
14	186	0.3	1	134 52
15	228	0.3	1	168 60
16	185	0.3	1	143 42
17	230	0.3	1	168 62
18	232	0.3	1	173 59
19	168	0.3	1	133 35
20	179	0.3	1	140 39
21	151	0.3	1	113 38
22	168	0.3	1	133 35
23	157	0.3	1	116 41
24	145	0.3	1	107 38
25	155	0.3	1	113 42
26	120	0.3	1	87 33
27	126	0.3	1	98 28
28	128	0.3	1	100 28
29	98	0.3	1	78 20
30	79	0.3	1	69 10
31	58	0.3	1	43 15
32	72	0.3	1	55 17
33	60	0.3	1	43 17
34	73	0.3	1	56 17
35	46	0.3	1	26 20
36	43	0.3	1	24 19
37	36	0.3	1	23 13
38	32	0.3	1	21 11
39	29	0.3	1	22 7
40	11	0.3	1	3 8
41	19	0.3	1	6 13
42	23	0.3	1	5 18
43	10	0.3	1	3 7
44	8	0.3	1	1 7
45	10	0.3	1	0 10
46	7	0.3	1	0 7
47	18	0.3	1	0 18
48	16	0.3	1	0 16
49	24	0.3	1	0 24
50	95	0.3	1	0 95
51	9528	0.3	1	4 9524


RUN STATISTICS FOR INPUT FILE: Samples/H3K4me3_Liver_A/raw_reads.fq.gz
=============================================
17143420 sequences processed in total
Sequences removed because they became shorter than the length cutoff of 20 bp:	10425 (0.1%)