Pigeon Tools Input

prepare

File Description
Transcript GFF Collapsed transcript GFF from isoseq collapse
Reference Annotation Reference annotation in GTF format
CAGE Peaks (Optional) CAGE peaks in BED format
Intropolis data (Optional) Intropolis data in custom format

classify

File Description
Reference Genome Reference genome in FASTA format
Reference Annotation Sorted and indexed (prepare) reference annotation in GTF format
CAGE Peaks (Optional) Sorted and indexed (prepare) CAGE peaks in BED format
Intropolis data (Optional) Sorted and indexed (prepare) Intropolis data in custom format
polyA motif list (Optional) polyA motif list in custom format
FL Counts (Optional) Single-cell IsoSeq FL count info from isoseq collapse (*.abundance.txt)
FL Counts (Optional) Bulk IsoSeq FL count info from isoseq collapse (*.flnc_counts.txt)

make-seurat

File Description
Molecules FASTA Molecules FASTA file from isoseq dedup
Groups txt file Groups text file from isoseq collapse

Examples

Sorted and indexed references for human and mouse can be found here.

Guidance about custom references can be found here.

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