Using the Tool - Output
This section describes all the output folders and files generated by SigProfilerMatrixGenerator.
Output Overview
| Mutation Type | Output Files |
|---|---|
| SBS (Single Base Substitution) | SBS6, SBS24, SBS96, SBS384, SBS1536, SBS6144 |
| DBS (Double Base Substitution) | DBS78, DBS186, DBS1248, DBS2976 |
| ID (Insertion/Deletion) | ID28, ID83, ID415, ID8628 |
| TSB (Transcriptional Strand Bias) | 24, 384, 6144 |
| CNV (Copy Number Variation) | CNV48 |
| SV (Structural Variants) | SV32 |
SBS: Single Base Substitution
| File | # of Sequences | Description |
|---|---|---|
| test.SBS6.all | 6 | 6 mutation types (C>A, C>G, C>T, T>A, T>C, T>G) |
| test.SBS24.all | 24 | 6 types × 4 transcriptional strand bias categories |
| test.SBS96.all | 96 | 4 × 6 × 4 (5' context × mutation × 3' context) |
| test.SBS384.all | 384 | 96 × 4 transcriptional strand bias categories |
| test.SBS1536.all | 1536 | Extended context (4 × 4 × 6 × 4 × 4) |
| test.SBS6144.all | 6144 | 1536 × 4 transcriptional strand bias categories |
For detailed explanation, see Output - SBS.
DBS: Double Base Substitution
| File | # of Sequences | Description |
|---|---|---|
| test.DBS78.all | 78 | Pyrimidine dinucleotide variants |
| test.DBS186.all | 186 | 78 + transcriptional strand bias categories |
| test.DBS1248.all | 1248 | 4 × 78 × 4 (with flanking context) |
| test.DBS2976.all | 2976 | 4 × 186 × 4 (with flanking context) |
For detailed explanation, see Output - DBS.
ID: Insertion/Deletion
| File | # of Sequences | Description |
|---|---|---|
| test.ID28.all | 28 | Basic indel classification |
| test.ID83.all | 83 | Extended indel classification with repeat/microhomology |
| test.ID415.all | 415 | 83 × 5 transcriptional strand bias categories |
| test.ID8628.all | 8628 | Complete indel sequence information |
For detailed explanation, see Output - ID.
TSB: Transcriptional Strand Bias
| File | # of Sequences | Description |
|---|---|---|
| strandBiasTest_24.txt | 24 | 6 × 4 categories |
| strandBiasTest_384.txt | 384 | 4 × 24 × 4 |
| strandBiasTest_6144.txt | 6144 | 4 × 384 × 4 |
Strand Bias Categories
- T - Transcribed strand
- U - Untranscribed strand
- N - Non-transcribed (intergenic)
- B - Bidirectional transcription
- Q - Questionable/ambiguous
For detailed explanation, see Output - TSB.
vcf_files Folder
Contains text-based files with original mutations paired with SigProfilerMatrixGenerator classifications:
| Subfolder | Description |
|---|---|
| DBS/ | Dinucleotide substitutions |
| MNS/ | Multinucleotide substitutions |
| SNV/ | Single nucleotide variants |
| ID/ | Small insertions and deletions |
For detailed explanation, see Output - vcf_files.
Plots Folder
Contains generated visualizations from SBS, DBS, and ID matrix generation:
Generated Plots
- SBS-6, SBS-24, SBS-96, SBS-384
- DBS-78, DBS-186
- ID-28, ID-83, ID-415
Additional Plots (via SigProfilerPlotting)
- SBS-1536
- Sample portraits
Each file contains a separate plot for every input sample analyzed.
More information about plot generation can be found at SigProfilerPlotting.