Trimming on Nanopore Data

Question

[santos48]

When I trim the adaptors is this beneficial to analysis of Nanopore ?

I trimmed the adaptors with Porechop, then I checking quality using FastQC then the average quality increased but, I saw overrepresented sequencing what should I do? Do you know of any tutorials on improving quality?

[WouterDeCoster]

is this beneficial to analysis of Nanopore

You tagged RNA-seq, but it is most likely important that you tell us more about what you aim to do.

For example, when just doing reference alignment and structural variant calling there is no need for trimming, and adapter sequences will get softclipped.

[santos48]

Thank you for answer, I will analyze it on clusters, functions, phylogeny. Should I trim it?

Answer 1

[colindaven]

You didn't say what kind of data you have. Genomic, bacterial ? Just align to genome.

It should be fine if you have used poretools and or guppy. FASTQC almost always mentions problems on all sorts of data.

PycoQC and Nanoplot/Nanofilt are decent quality control options more suited to ONT data.

[santos48]

These are genomic data. I checked with FASTQC because I don't have a sequencing_summary.txt file. I did not know about the quality check with Nanoplot/Nanofilt. I will look at it thank you