After transcript sequences are mapped to a reference genome,
isoseq3 collapse can be used to collapse redundant transcripts (based on exonic structures) into unique isoforms. Output consists of unique isoforms in GFF format and secondary files containing information about the number of reads supporting each unique isoform.
Map reads using pbmm2 before collapsing
pbmm2 align --preset ISOSEQ --sort <input.bam> <ref.fa> <mapped.bam>
Collapse mapped reads into unique isoforms using isoseq collapse.
isoseq3 collapse <mapped.bam> <collapse.gff>
isoseq3 collapse by default will collapse isoforms containing 5p degradation as of version
3.8.0. To turn this off
--do-not-collapse-extra-5exons should be used. This option is recommended for bulk IsoSeq.
collapse.gffcontains the collapsed isoforms in gff format.
*.abundance.txtcontains information about the number of FLNC reads supporting each isoform and cell barcodes if applicable. Each unique isoform has the ID format PB.X.Y, while
count_fldenotes the number of unique molecules (after UMI deduplication) supporting the isoform, and
fl_assocdenotes the number of reads (before UMI deduplication) supporting it.
cell_barcodesshows the list of single cell barcodes from which the reads came from, if applicable.
pbid count_fl fl_assoc cell_barcodes PB.1.1 2 2 ATCCATTCACCTCTGT,ATCGGCGCAGAGATGC PB.2.1 1 1 CGGACACCATTGCCGG PB.3.1 1 1 ACTTCGCGTCTAACTG
*.group.txtshows the grouping of redundant isoforms (based on mapped exonic structures), where the read names
molecule/<number>denote a unique molecule after UMI deduplication.
PB.1.1 molecule/7343975,molecule/7738347 PB.2.1 molecule/14601188 PB.3.1 molecule/3998518
*.read_stat.txtshows the assignment of each read (before UMI deduplication) to the final, unique isoforms PB.X.Y. Read names with the format
<movie>/<zmw>/ccsindicate a CCS read, whereas
<movie>/<zmw>/ccs/<start>_<end>further denotes a segment of a CCS read (S-read), likely as a result of segmentation (using, for example, Skera) of concatenated single cell libraries.
id pbid m64012_220421_000242/120719489/ccs/10460_11196 PB.1.1 m64012_220421_000242/17565024/ccs/13918_14203 PB.1.1 m64012_220421_000242/161089449/ccs/1955_2888 PB.2.1 m64012_220421_000242/158664505/ccs/2488_2901 PB.3.1
As of isoseq3 v3.8.0
isoseq3 collapse has algorithmic updates. These updates include performance improvements and updates to isoform collapse logic.
What is new in v3.8.0 and later?
Collapsing extra 5p exons
For applications like single-cell IsoSeq where there is a higher percentage of 5p truncated isoforms, it is useful to collapse isoforms that have a matching exon structure with the exception of extra 5p exons. Previous versions of
collapse did not merge isoforms with extra 5p exons. As of v3.8.0,
collapse will merge these isoforms by default. To not allow merging isoforms with extra 5p exons, use
--do-not-collapse-extra-5exons. This option is used in the bulk IsoSeq workflow.
Flexible first/last exon differences
Previous versions of
collapse used stringent maximum differences (5bp) for both internal junctions and external junctions. As of v3.8.0, the maximum 5p and 3p differences have been increased and paramaters added to allow adjustments. Note: the maximum 5p difference only applies when
--do-not-collapse-extra-5exons is set.
collapse maximum junction difference parameters:
--max-fuzzy-junction INT Ignore mismatches or indels shorter than or equal to N.  --max-5p-diff INT Maximum allowed 5' difference if on same exon.  --max-3p-diff INT Maximum allowed 3' difference if on same exon. 
What if I want to use the legacy
collapse logic can be recreated using the following parameters:
isoseq3 collapse --do-not-collapse-extra-5exons --max-5p-diff 5 --max-3p-diff 5 <mapped.bam> <collapsed.gff>