How do I interpret the adapter output from FastQC?

Question

[Endre Bakken Stovner]

Here is the output I get from fastqc:

>>Adapter Content       pass
#Position       Illumina Universal Adapter      Illumina Small RNA Adapter      Nextera Transposase Sequence
1       0.001025        0.0     0.0
2       0.001025        0.0     0.0
3       0.001025        0.0     0.0
4       0.001025        0.0     2.5E-5
5       0.001025        0.0     2.5E-5
6       0.001025        0.0     2.5E-5
7       0.001025        0.0     2.5E-5
8       0.001025        0.0     2.5E-5
9       0.001025        2.5E-5  2.5E-5
10      0.001025        5.0E-5  2.5E-5
11      0.001025        5.0E-5  5.0E-5
12      0.001025        5.0E-5  5.0E-5
13      0.001025        5.0E-5  5.0E-5
14      0.001025        5.0E-5  5.0E-5
15      0.001025        5.0E-5  1.0E-4
16      0.001025        5.0E-5  1.25E-4
17      0.001025        5.0E-5  1.25E-4
18      0.001025        5.0E-5  1.5E-4
19      0.001075        7.5E-5  1.5E-4
20      0.001125        7.5E-5  1.5E-4
21      0.00115 7.5E-5  1.5E-4
22      0.00115 7.5E-5  1.5E-4
23      0.001225        7.5E-5  1.5E-4
24      0.0013  7.5E-5  1.75E-4
25      0.001475        7.5E-5  1.75E-4
26      0.00175 1.0E-4  2.0E-4
27      0.0024  1.0E-4  2.0E-4
28      0.0039  1.25E-4 2.0E-4
29      0.006525        1.25E-4 2.0E-4
30      0.01045 1.25E-4 2.0E-4
31      0.017425        1.5E-4  2.0E-4
32      0.02815 1.5E-4  2.5E-4
33      0.044625        1.5E-4  2.75E-4
34      0.07035 1.5E-4  3.5E-4
35      0.1024  1.5E-4  3.5E-4
36      0.1457  1.5E-4  3.75E-4
37      0.20115 1.5E-4  4.0E-4
38      0.267825        1.5E-4  4.0E-4
39      0.346775        1.5E-4  4.0E-4
>>END_MODULE

What does this mean? And if it means there are adapters still in my data, how do I get their sequences - I need to remove them with cutadapt.

I'm guessing it means there are no adapters, because otherwise it would be strange not to list them.

Answer 1

[Brian Bushnell]

According to that, you have 0.35 adapter content by position 39, of Illumina Universal Adapters. The header does not say whether this is percent or not; probably it means 0.35%.

The BBMap package contains a file adapters.fa in the /ref/ subdirectory which contains this adapter sequence (and all other official Illumina adapter sequences). This can be used with cutadapt, or with the included adapter-trimming tool, BBDuk.

[Endre Bakken Stovner]

Thanks; will look into it.