How do I interpret the adapter output from FastQC?
1
0
Entering edit mode
8.7 years ago

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.

FastQC • 2.7k views
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1
Entering edit mode
8.7 years ago

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.

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Entering edit mode

Thanks; will look into it.

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