Software for detecting adaptors

[karinlag]

Hi!

I have MiSeq sequences which have been produced using the Hyper Kapa Plus protocol. However, the lab does not know and/or does not know what adapter set it used. So, what software would you use to identify and detect adapters in a read set?

[Kacper]

fastqc? is you have own adapters dataset you could add own sequences...

[karinlag]

fastqc? is you have own adapters dataset you could add own sequences...

The problem is that I don´t know which adapters were used. I would like to figure out how to figure out which ones were used, so that I can then afterwards trim them out.

[GenoMax]

When not known, you can scan against a collection of common ones (like those found in "adapters.fa" file in the resources directory of BBMap suite). I will also recommend that you try bbduk.sh (part of BBMap) for data trimming.

[Kacper]

When not known, you can scan against a collection of common ones (like those found in "adapters.fa" file in the resources directory of BBMap suite). I will also recommend that you try bbduk.sh (part of BBMap) for data trimming.

you have same information (or you could create) in FastQC/Configuration
adapter_list.txt/contaminant_list.txt to figure out which ones were used

[Markiyan]

Try locating reads matching each other and going into the adapter.

To detect novel adapter sequences,

You can look at:

1. Kmer plot in fastqc (set -k 9 or -k 10).

2. You can also look for the match of the reverse complement of the first 25-32 bps of the R2 in the R1, and see what sequence follows it.
(can be done with perl).

PS: For a quick final findings confirmation/adapter consensus selection "grep -c [sequence]" is the tool of choice...