Name Version Build Channel
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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
Operating system
Package name
isoseq collapse2
Conda environment
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 alignflnc.bam
directly to reference?Error message NA
To Reproduce
Expected behavior Bam file with aligned transcripts for
stringTie2
input