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