Question: Use kallisto with ONT (nanopore) cDNA long reads
1
gravatar for Nicolas Rosewick
2.6 years ago by
Belgium, Brussels
Nicolas Rosewick8.6k wrote:

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 • 1.4k views
ADD COMMENTlink written 2.6 years ago by Nicolas Rosewick8.6k

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

GMAP works very well for Nanopore cDNA sequencing.

ADD REPLYlink written 2.6 years ago by WouterDeCoster42k

Will it take the quality into account for the mapping ?

ADD REPLYlink written 2.6 years ago by Nicolas Rosewick8.6k
2

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 REPLYlink written 2.6 years ago by WouterDeCoster42k

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 REPLYlink modified 2.6 years ago • written 2.6 years ago by Nicolas Rosewick8.6k

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 REPLYlink written 14 months ago by caggtaagtat930
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