Question: Use kallisto with ONT (nanopore) cDNA long reads
0
gravatar for Nicolas Rosewick
21 months ago by
Belgium, Brussels
Nicolas Rosewick7.5k 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 • 1.0k views
ADD COMMENTlink written 21 months ago by Nicolas Rosewick7.5k

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 21 months ago by WouterDeCoster38k

Will it take the quality into account for the mapping ?

ADD REPLYlink written 21 months ago by Nicolas Rosewick7.5k
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 21 months ago by WouterDeCoster38k

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 21 months ago • written 21 months ago by Nicolas Rosewick7.5k

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 4 months ago by caggtaagtat500
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