Nanopore Preprocessing Step

Question

[santos48]

When I analyze Nanopore reading, should I analyze each file individually(I have over 1000 .fastq files) or combine it with the cat command to analyze it.

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?

If you know anything on that topic can you share that articles?

Thank you

Answer 1

[Steven Lakin]

You can concatenate them using cat and analyze the aggregated file. You could also analyze them individually if you wish; each read is independent.

[santos48]

thank you for your answer,

[Ram]

If an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one answer if they work. This will help future users that might find this post find the right answer.