How to figure out adapter sequences in RNA seq?

Question

[bioinfo]

Hello,

I am trying to understand where do the adapter sequences that need to be trimmed from the data come from? Do they come from the kits that are used to prepare the library? For example, if I switch from a truseq kit to a kapa hifi kit would I need to use different sequences for adapter trimming? I would be using the same Illumina machine for the run.

Thank you

Answer 1

[rfran010]

Yes, the adapter sequence comes from the library prep kit. Generally, during the ligation step you are ligating the adapter. Different kits will often use different adapter sequences and should be provided in the manuals. But, you can also usually identify the adapters from the sequencing output directly as GenoMax linked.

Answer 2

[GenoMax]

would I need to use different sequences for adapter trimming

Potentially. You can find two solutions here: Identify adapter sequences for trimming from Illumina paired end fastq files