Pigeon classify and filter output

Classification File

The classify and filter tools output a txt file containing isoform annotation information. The output from classify and filter will have the extensions _classification.txt or _classification.filtered_lite_classification.txt respectively. Both of these outputs follow the SQANTI3 classification file convention with the exception of two added columns.

Column Description
fl_assoc FL count associated with the isoform including PCR duplicates.
cell_barcodes Comma separated list of unique cell barcode ids associated with the isoform.

Junction File

The classify tool outputs a txt file containing every junction for each isoform (_junctions.txt) following the SQANTI3 junction file convention.

Filtered Reasons File

The filter tool outputs a txt file containing the reasons an isoform was filtered.

Reasons an isoform can be filtered:

Reason Description
IntraPriming The primer was annealing to downstream A-rich regions.
Mono-Exonic The isoform contains a single exon.
RTSwitching There is an artifact of reverse transcriptase template switching.
LowCoverage/Non-Canonical There is a low sample coverage for splice sites that are not in the known “canonical” set of splice sites.

Example:

# classification: sample_classification.txt
# isoform: ????????
# intrapriming cutoff: 0.6
# min_cov cutoff: 3
filtered_isoform,filter
PB.1.1,IntraPriming
PB.1.6,LowCoverage/Non-Canonical
PB.1.7,IntraPriming
PB.5.1,LowCoverage/Non-Canonical
PB.6.1,LowCoverage/Non-Canonical

Pigeon report output

The report tools outputs a txt file containing the read count and number of unique genes found in a subsampled number of reads.

Pigeon make-seurat output

The make-seurat tool outputs the required files to run tertiary analysis with Seurat.

Files output:

<output_dir>/annotated.info.csv
<output_dir>/info.csv
<output_dir>/genes_seurat/barcodes.tsv
<output_dir>/genes_seurat/genes.tsv
<output_dir>/genes_seurat/matrix.mtx
<output_dir>/isoforms_seurat/barcodes.tsv
<output_dir>/isoforms_seurat/genes.tsv
<output_dir>/isoforms_seurat/matrix.mtx

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