Best practice: pTrimmer before read QC or after?

DMU-lilab / pTrimmer

Used to trim off the primer sequence from mutiplex amplicon sequencing

GNU General Public License v3.0

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Best practice: pTrimmer before read QC or after? #25

Open jacaravas opened 3 months ago

jacaravas commented 3 months ago

Hello,

Is there a best practice for running pTrimmer alongside a read level quality trimmer such as "fastp"? Is running pTrimmer upstream of read QC the best way to ensure that primer sequences are removed?

XLZH commented 3 months ago

@jacaravas I suggest running ptrimmer prior to other quality control software. The reason is that some software may damage the primer sequences when processing the READ, resulting in the incomplete removal of primers for certain sequences.

If there are any other issues during the primer removal process, please feel free to contact me!

best, xiaolong zhang

jacaravas commented 3 months ago

@XLZH Thank you!