Differential gene expression analysis with MinIon reads

[Diegodescarpates]

Dear all,

I tried to adapt RNA-seq pipeline's analysis to Minion 2D reads (eg Cufflinks) for differential gene expression analysis. I met some errors during processing. I arrived to get around some of them but finally I can not use results.

Do some of you know functional pipelines for MinIon reads ? Thanks a lot in advance.

Regards, D

[Diegodescarpates]

An inspired person ?

[GenoMax]

Not sure what you mean by "can not use results".

What do the alignments look like? Are the alignments restricted to individual genes or do they go past the gene boundaries? What kind of depth are you observing?