Question on Quantification & Differential Expression Workflow

[MGordon09]

Operating system

NAME="Rocky Linux"
VERSION="8.9 (Green Obsidian)"
ID="rocky"
ID_LIKE="rhel centos fedora"
VERSION_ID="8.9"
PLATFORM_ID="platform:el8"
PRETTY_NAME="Rocky Linux 8.9 (Green Obsidian)"
ANSI_COLOR="0;32"
LOGO="fedora-logo-icon"
CPE_NAME="cpe:/o:rocky:rocky:8:GA"
HOME_URL="https://rockylinux.org/"
BUG_REPORT_URL="https://bugs.rockylinux.org/"
SUPPORT_END="2029-05-31"
ROCKY_SUPPORT_PRODUCT="Rocky-Linux-8"
ROCKY_SUPPORT_PRODUCT_VERSION="8.9"
REDHAT_SUPPORT_PRODUCT="Rocky Linux"
REDHAT_SUPPORT_PRODUCT_VERSION="8.9"

Package name
isoseq collapse2

Conda environment

  Name    Version  Build       Channel 
─────────────────────────────────────────
  isoseq  4.0.0    h9ee0642_0  bioconda

Describe the bug
I have a general question on IsoSeq workflow. I have virus-infected cells with 3 viral variants (and reps for each condition) I want to look at differential expression of viral transcripts in addition to host transcript isoform analysis. My question is should I skip the isoseq3 cluster for viral DEA and align flnc.bam directly to reference?

Error message
NA

To Reproduce

lima
isoseq 
isoseq3 refinement
isoseq3 cluster (??)
pbmm2

Expected behavior
Bam file with aligned transcripts for stringTie2 input

[armintoepfer]

Please reach out to support@pacb.com, as we can only help you with technical issues. Thank you.