Getting Started

Command Description Output format
lima Remove cDNA primers fl.bam
isoseq refine Remove polyA tail and artificial concatemers flnc.bam
isoseq cluster2 De novo isoform-level clustering scalable to large number of reads (e.g. 40-100M FLNC reads) clustered.bam
pbmm2 Align to the genome mapped.bam
isoseq collapse Collapse redundant transcripts based on exonic structures collapsed.gff
pigeon classify Classify transcripts against annotation GFF and TXT files
pigeon filter Filter transcripts for potential artifacts GFF and TXT files

Begin with the bulk workflow which ends at isoseq cluster, then continue to pigeon workflow for transcript mapping, collapse, and classification.

Command Description Output format
lima Remove cDNA primers fl.bam
isoseq tag Extract UMI and cell barcodes flt.bam
isoseq refine Remove polyA tail and artificial concatemers flnc.bam
isoseq correct Correct cell barcodes and tag reads that are real cells corrected.bam
isoseq bcstats Summarize barcode statistics for real/non-real cells bcstats_report.tsv
isoseq groupdedup Deduplicate reads dedup.bam
pbmm2 Align to the genome mapped.bam
isoseq collapse Collapse redundant transcripts based on exonic structures collapsed.gff
pigeon classify Classify transcripts against annotation GFF and TXT files
pigeon filter Filter transcripts for potential artifacts GFF and TXT files
pigeon make-seurat Make gene- and isoform-level matrices MTX and TSV files

Begin with the single cell-specific worfklow which ends at isoseq groupdedup, then continue to pigeon workflow for transcript mapping, collapse, and classification.

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