cutadapt vs porechop

Question

[KVC_bioinfo]

Hello All,

I have been trying to trim rna-seq reads (1D^2) from Oxford nanopore technology for adaptors.

I tried using cutadapt which trimmed only 2% of reads. (1D and 1D^2) However, porechop trimmed ~95% 1D and ~60% 1d^2.

I am unable to understand why there is such a huge difference?

Any help is greatly appreciated. TIA

Answer 1

[WouterDeCoster]

Cutadapt is developed for accurate Illumina data and therefore will look for exact matches to expected adapters (or very accurate). porechop is made for noisier nanopore data so will tolerate more mismatches.

[KVC_bioinfo]

Thank you very much!