How to remove adapter clean? about fastp

[sfchen]

1, can you upload the first 10000 lines of the two files?
2, did Trimmomatic or Cutadapt cut adapters clean?

Thanks

[haiwufan]

Hi sfchen,
Test file :
Test.zip

In my test, Trimmomatic or cutadapt cut adapter clean.

[sfchen]

But why they cut less adapters?

[haiwufan]

In my opinion, fastp remove adapters by overlap, that's not efficient method.
cutadapt and trimmomatic cut adapter by string match, that's the different with fastp.

[sfchen]

Thanks for your opinion, the method for fastp to cut adapters for SE data is similar as cutadapt and trimmomatic. For PE data, we use overlap analysis since we think it's more efficient and faster.

but I need to understand why cutadapt and trimmomatic cut less adapters as I know from the table, but you said their result are cleaner?

[haiwufan]

maybe my description is not clear, I can share my perl script to you.
stat_adapter.pl.txt

[sfchen]

Thanks.

For the test.zip you uploaded, could you upload the processed data with Trimmomatic and Cutadapt?

So I can do an analysis.

[haiwufan]

sfchen,
I run test data with cutadapt, trimmomatic, fastp.
01_Cutadapt.tar.gz
01_Fastp.tar.gz
01_Trimmomatic.tar.gz

[sfchen]

Thank you very much! I will test and update.

[yangyi0000]

Hi sfchen, I'm curious about the question,too. But this issue is closed, where can I access to the results please?