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