Low quality fast5 files

Low quality fast5 files

0

Hi,

I performed direct RNA Seq (with polyA) to my short sequences (~90 bp).
However, my fastq_pass are only 20% of the total reads.

I used this quality script to do analysis for the quality score: https://gist.github.com/wdecoster/7cad6080950fa1e3ae3eaeeac4f6ae4d#file-perbasesequencecontentandquality-py

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Do you have experience/thoughts for why I am observing such fluctuating qualities through the read body?

I appreciate your feedback.
Thanks!


fast5


basequality


fastq


nanopore

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