# Do I have to remove overlapping reads from paire\_end data before Metahplan?

**URL:** <https://forum.biobakery.org/t/do-i-have-to-remove-overlapping-reads-from-paire-end-data-before-metahplan/7615>\
**Category:** KneadData\
**Created:** [November 27, 2024, 3:55pm UTC](https://forum.biobakery.org/t/do-i-have-to-remove-overlapping-reads-from-paire-end-data-before-metahplan/7615 "2024-11-27T15:55:32Z")\
**Posts on this page:** 1\
**Page:** 1

<div class="post-metadata">

**Author:** ![Michela\_Francesconi](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/michela_francesconi/32/2874_2.png) [@Michela\_Francesconi](https://forum.biobakery.org/u/Michela_Francesconi)\
**Post date:** [November 27, 2024, 3:55pm UTC](https://forum.biobakery.org/t/do-i-have-to-remove-overlapping-reads-from-paire-end-data-before-metahplan/7615/1 "2024-11-27T15:55:32Z")

</div>

I have paired\_end files from shoutgun metagenomics analysis (251 bp). Before starting with Metaphan, I run fastqc and fastq\_screen to check how my files are.  
I used KneadData to delete the human genome, and now it is ok. (I also notice that all my files do not pass the “Per Base Sequence Content.” Is this a problem? All the other control is OK.)

Should I also have to delete overlapping reads between R1 and R2? How can I do it? I try your preprocessing.py file in Python, but I do not understand the difference with KneadData. Can you help me?

Thanks  
Michela