Adapter trimming using fastp
Hi everyone.
I use Trimmomatic for adapter trimming, but plan to use fastp in the future.
Adapter trimming with Trimmomatic allows us to specify seed mismatches, palindrome clips threshold, simple clip threshold, minAdapterLength, as in the following example:
ILLUMINACLIP:./Trimmomatic-0.39/adapters/NexteraPE-PE.fa:2:30:10:2
How can I specify the same conditions with fastp?
If you have any commands or scripts, I would appreciate it if you could let me know.
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Since these tools trim using different approaches I don't think you can translate that command to
fastpone to one. These approaches being quoting from the fastp paper:The fastp paper has benchmarks against Trimmomatic. I suggest you create a small test set and try out different parameters and see if they output your desired results. Here is a video demonstrating various fastp parameters.
Thank you for your reply! Your advice is very helpful. I would like to try different parameters as you mentioned.