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Transcriptome long-read sequencing (ONT)

Dear community,

I sequenced transcriptome (cDNA-PCR Sequencing Kit) using Nanopore long-read sequencing technology (flow-cell R9.4.1).

I have a question regarding a low Quality score (below 9), which caused that 3.84 Gb were classified as "FAIL", and only 1.68 Gb as "PASS". Since we are only optimizing the protocol, the first sequencing was done on an expired flow-cell. However, translocation speed was sufficient throughout the experiment.

Can be low Q score a result of the expired flow-cell or are there any other explanations for this?

Thank you in advance!

Kind regards.

ont
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updated by Ram Ram • written by htrcek • htrcek

Have you checked the "failed" sequences by aligning them if you have a reference available? Those may still be usable.

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written by GenoMax GenoMax

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