please what the differences between the using of cutadapt option and trimmomatic when we want to do trimming after checking the quality score?
I will appreciate your help
Hi @kebabiness_over9000,
according to this paper, both tools perform similarly regarding data quality after processing. However, you should take into account that Trimmomatic is specifically designed for processing Illumina paired-end and single-ended data. If your datasets have been generated by using a different technology, you should use Cutadapt.
Regards
gallardoalba https://help.galaxyproject.org/u/gallardoalba
August 29Hi @kebabiness_over9000
https://help.galaxyproject.org/u/kebabiness_over9000,
according to this paper
https://www.frontiersin.org/articles/10.3389/fbioe.2020.00817/full,
both tools perform similarly regarding data quality after processing.
However, you should take into account that Trimmomatic is specifically
designed for processing Illumina paired-end and single-ended data
https://github.com/usadellab/Trimmomatic#running-trimmomatic. If your
datasets have been generated by using a different technology, you should
use Cutadapt.Regards
Visit Topic https://help.galaxyproject.org/t/trimming-sequence/6552/2
Many thanks
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