Adapter Removing

Question

[daffodil]

Hi everybody,

Should I remove the adapter if the fastqc results in such data as the yellow alarm?

Best regards

[Ram]

Please show us FASTQC results from before and after adapter trimming. "Yellow alarm" is nowhere near enough detail.

[daffodil]

this one from before trimming.

[daffodil]

Please let me know should I have removed the adapter from this file?

Answer 1

[GenoMax]

If you are planning to do any de novo work then you should scan/trim the data. It does not take long to scan and trim so do it to ensure there is no extraneous sequence left.

As a side note: an aligner will softclip the adapters during alignment so that should address any adapter present.

Answer 2

[a.alnawfal.1992]

Hi Daffodil,

If adapters are identified in your sequencing reads, they should be removed. Why would you consider leaving them in? I'm curious. Is your library preparation kit the Illumina Nextera?

Personally, I do scan and trim adapter "since it is not a bottleneck in the analysis" rather than leave it for the aligner. also, I prefer using Fastp over FastQC for inspecting the quality of reads and then performing any necessary corrective actions. Fastp can handle both tasks in one go, and you can also control its behavior. Below is the basic command for Fastp:

fastp -i in.R1.fq.gz -I in.R2.fq.gz -o out.R1.fq.gz -O out.R2.fq.gz

Remember, adapter trimming is enabled by default. Please refer to the Fastp repository for more information: Here

[daffodil]

Thank you so much.

[daffodil]

My library prepared by the Illumina Nextera. As you mentioned for fastp adapter trimming is enabled by default, however should I add the nextra illumena adapter in the comand ("-a CTGTCTCTTATACACATCT -A CTGTCTCTTATACACATCT ")?

[a.alnawfal.1992]

Sorry for the late reply. No, you should not do that. It will be auto-detected and trimmed. Adding the adapter will make the process take longer to finish