Use kallisto with ONT (nanopore) cDNA long reads

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7.3 years ago

Nicolas Rosewick 11k

Hi,

I've some cDNA sequences from an nanopore experience. In my knowledge there is not yet splice-aware aligner for such type of data. Thus is it possible to use kallisto to infer the TPM and estimate read count for each cDNA sequence ?

Thanks

nanopore kallisto long reads • 3.5k views

ADD COMMENT • link 7.3 years ago by Nicolas Rosewick 11k

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In my knowledge there is not yet splice-aware aligner for such type of data.

GMAP works very well for Nanopore cDNA sequencing.

ADD REPLY • link 7.3 years ago by WouterDeCoster 47k

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Will it take the quality into account for the mapping ?

ADD REPLY • link 7.3 years ago by Nicolas Rosewick 11k

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As far as I know yes, it does.

An alignment looks like this:

enter image description here

Note that alignment was performed without specifying gene annotation and it nicely recapitulates the known exon structure.

ADD REPLY • link 7.3 years ago by WouterDeCoster 47k

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ok thanks I didn't know gmap could hande error-prone ONT reads. I'll give a shot.

For kallisto, I will try also.

ADD REPLY • link 7.3 years ago by Nicolas Rosewick 11k

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Hi, so 16 months later I wanted to ask you Nicolas Rosewick, if it was possible/ok to align those reads with a software like kalisto?

ADD REPLY • link 5.9 years ago by caggtaagtat ★ 1.9k

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