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Getting Started

Command Description Output format
lima Remove cDNA primers fl.bam
isoseq3 refine Remove polyA tail and artificial concatemers flnc.bam
isoseq3 cluster De novo isoform-level clustering unpolished.bam
pbmm2 Align to the genome mapped.bam
isoseq3 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 isoseq3 cluster, then continue to pigeon workflow for transcript mapping, collapse, and classification.

Command Description Output format
lima Remove cDNA primers fl.bam
isoseq3 tag Extract UMI and cell barcodes flt.bam
isoseq3 refine Remove polyA tail and artificial concatemers flnc.bam
isoseq3 correct Correct cell barcodes and tag reads that are real cells corrected.bam
isoseq3 bcstats Summarize barcode statistics for real/non-real cells bcstats_report.tsv
isoseq3 groupdedup Deduplicate reads dedup.bam
pbmm2 Align to the genome mapped.bam
isoseq3 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 isoseq3 groupdedup, then continue to pigeon workflow for transcript mapping, collapse, and classification.


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