Isoseq collapse : collapsing extra 5p exons results in incorrect isoforms.

[Fougere87]

Operating system UNIX

Package name isoseq

Describe the bug We performed single cell RNA sequencing using 10x 5p captures, Mas Isoseq library preparation and sequencing on Revio system. Everything is working fine, but for some genes I have a dominant isoform that has one extra exon that does not exist. This extra exon is included in the isoform even if it is present in only one read (over more that 15000).
After filtering this isoform is discarded (considered as RTS) and the counts of the gene are near 0... Maybe adding a threshold including a minimal coverage to keep or not an extra exon and collapse it to FSM isoform would be helpful.