iso-seq reads and pbfusion

[meryyr]

Hi!
Pbfusion uses aligned Iso-Seq reads. Does this mean that I can use flnc.bam reads (generated from the Iso-Seq pipeline), aligne them to hg38 using the pbmm2 tool (pbmm2 index --preset ISOSEQ and pbmm2 align --preset ISOSEQ), and then run pbfusion on the aligned flnc reads?

Or is it mandatory to cluster the flnc.bam reads first with the isoseq cluster2 tool, then align the clustered reads, and lastly perform the pbfusion?

Thank you for the help! :)

[zeeev]

Hi @meryyr,

I'd recommend that you start with the FLCN reads. The tool also works on the clustered reads, however, we find better performance using the reads. The distribution of reads allows us to capture variability in mapping.

[meryyr]

Hi @meryyr,

I'd recommend that you start with the FLCN reads. The tool also works on the clustered reads, however, we find better performance using the reads. The distribution of reads allows us to capture variability in mapping.

Thank you!!