# Total reads after trimming is the SAME as Initial number of reads

**URL:** <https://forum.biobakery.org/t/total-reads-after-trimming-is-the-same-as-initial-number-of-reads/4607>\
**Category:** KneadData\
**Created:** [January 5, 2023, 7:00pm UTC](https://forum.biobakery.org/t/total-reads-after-trimming-is-the-same-as-initial-number-of-reads/4607 "2023-01-05T19:00:30Z")\
**Posts on this page:** 1\
**Page:** 1

<div class="post-metadata">

**Author:** ![fsaravia](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/fsaravia/32/716_2.png) [@fsaravia](https://forum.biobakery.org/u/fsaravia)\
**Post date:** [January 5, 2023, 7:00pm UTC](https://forum.biobakery.org/t/total-reads-after-trimming-is-the-same-as-initial-number-of-reads/4607/1 "2023-01-05T19:00:30Z")

</div>

Tool:  
kneaddata v0.12.0

I notice that the total reads after trimming are the same as the initial number of reads. I am not sure what parameters would need to be adjusted or what may be causing this. **Is this something to be concerned about?**  
The final number of reads (paired\_1/2.fastq files) are different so I know that QC is being performed.

As an example,

- Initial number of reads R1: 4038815.0
- Total reads after trimming 1: 4038815.0
- Toal reads paired\_1: 3993709.0

```auto
for sample in `cat samples.txt`; do
kneaddata -i1 rawseqs_QCinput/$sample*R1* -i2 rawseqs_QCinput/$sample*R2* -o kneaddata --threads 10 --max-memory=1000m \
--reference-db /data/databases/human/ \
--trimmomatic=/data/Microbiome/RefData/Metagenomics/biobakery_workflows_databases/Trimmomatic-0.39/ \
--trimmomatic-options ILLUMINACLIP:TruSeq3-PE.fa:2:30:10:2:TRUE \
--sequencer-source TruSeq3 \
--trf /home/fsaravia/.conda/pkgs/trf-4.09.1-hec16e2b_2/bin/
done

```