Trim Galore: Automatic detection of adapters

Question

[Daniel]

Hello!

I have what should be a straightforward but possibly stupid question (sorry). In this trim_galore user guide provided by Barbraham Bioinformatics, they mention that:

To control the stringency of the adapter removal process one gets to specify the minimum number of required overlap with the adapter sequence; else it will default to 1. This default setting is extremely stringent, i.e. an overlap with the adapter sequence of even a single bp is spotted and removed.

I don't understand what an overlap of 1 bp means. If the adapter sequence has all 4 nucleotides, wouldn't any sequence have an overlap of 1? Thus, under default settings wouldn't all reads be trimmed?

If my logic is correct, are they doing this to force users to select an adapter threshold?

Thank you.

Answer 1

[inedraylig]

You will notice that in the paragraphs before the one quoted, the manual notes that an adapter is expected at the first 12bp or 13 of a sequence. trim_galore begins by looking for an adapter at the start of a sequence and truncates the sequence to remove the adapter. If the adapter is not found, only then it seeks a partial match. So if the first bp of a sequence matches the adapter, it will be truncated, and if the first 2bp match - they will be removed, etc. It does remove one or a few more bp from any sequence regardless of the adapter content, but a lose of a few bp from each read can be acceptable for most pipelines (or adjusted manually if not).

[Daniel]

Got it, this clears things up. Thank you!