Use kallisto with ONT (nanopore) cDNA long reads

Question

[Nicolas Rosewick]

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

[WouterDeCoster]

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

GMAP works very well for Nanopore cDNA sequencing.

[Nicolas Rosewick]

Will it take the quality into account for the mapping ?

[WouterDeCoster]

As far as I know yes, it does.

An alignment looks like this:

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

[Nicolas Rosewick]

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

For kallisto, I will try also.

[caggtaagtat]

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?