Unexpected Chain Samples Results about cdna_cupcake

[Magdoll]

Hi @j-baller ,

The count file numbers (fields like count_fl, count_nfl), show the number of supporting full-length/non-full-length CCS reads. Since each CCS read is a single molecule, it shows the number of supporting single molecules.

I don't know what your input to chaining is, but I am assuming it is NOT CCS reads but rather after running Iso_Seq cluster, you obtain the HQ (high-quality) isoforms, correct?

Each HQ isoform is the polished consensus of a "cluster" of FL and nFL CCS reads. Hence, each HQ isoform itself is usually supported by multiple (single molecule) reads.

The count file doesn't show the number of supporting HQ isoforms - that number is rather meaningless - rather, it shows for each unique isoform (I assume you mapped the HQ isoforms to a genome and collapsed them) the number of supporting CCS (single molecule) reads.

If this is still confusing, or you would like to confirm you are indeed looking at CCS reads as counts, please send me some more detail about what went into your chaining? What are the sequence IDs?

--Liz

[j-baller]

Hi Liz,
Your response makes perfect sense. I had forgotten about the inclusion of the cluster_report as a source of CCS reads.

Thank you for your response,
Josh