read count for RNA sequencing via nanopore
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4 months ago
gat • 0

Hi all,

I have some long reads sequencing data of Oxford nanopore technology. I mapped reads to the human genome via minimap2, mapping makes sense but as expected, there are many seq errors and gap openings. Now I want to have read count per gene. For this end I tried to run Salmon, using an indexed human transcriptome, but most of the reads were filtered out due to low alignment score.

What is the best practice for RNA-seq quantification of long read data?

thanks a lot! Gat.

long RNA-seq gene expression reads read count • 336 views
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Have you checked the pipeline provided by ONT?

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GenoMax makes a good suggestion. Generally the next step would be use of a tool like FeatureCounts or htseq-count to get the read counts.

AFAIK Salmon is a kmer tool intended for short reads, so not applicable here.

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