Using SigProfilerMatrixGenerator - Output

This section goes over all the output folders and files in detail.

SBS: Single Base Substitution

The calculations for the number of returned sequences in the SBS output folder are summarized below.

File	# of sequences
test.SBS6.all	6
test.SBS24.all	6 x 4 = 24
test.SBS96.all	4 x 6 x 4 = 96
test.SBS384.all	96 x 4 = 384
test.SBS1536.all	4 x 4 x 6 x 4 x 4 = 1536
test.SBS6124.all	1536 x 4 = 6124

For a more detailed explanation, refer to the Output - SBS page.

DBS: Double Base Substitution

The calculations for the number of returned sequences in the DBS output folder are summarized below.

File	# of sequences
test.DBS78.all	78
test.DBS312.all	186
test.DBS1248.all	4 x 78 x 4 = 1248
test.DBS4992.all	4 x 186 x 4 = 2976

For a more detailed explanation, refer to the Output - DBS page.

ID: Insertion Deletion

The calculations for the number of returned sequences in the DBS output folder are summarized below.

File	# of sequences
test.ID28.all	28
test.ID83.all	83
test.ID415.all	83 x 5 = 415
test.ID8268.all	8268

For more details, refer to the Output - ID page.

TSB: Transcriptional Strand Bias

The calculations for the number of returned sequences in the TSB output folder are summarized below.

File	# of sequences
strandBiasTes_24.txt	6 x 4 = 24
strandBiasTes_384.txt	4 x 24 x 4 = 384
strandBiasTes_6144.txt	4 x 384 x 4 = 6144

For a more detailed explanation, refer to the Output - TSB page.

vcf_files

The vcf_files folder contains the following additional folders depending on the input parameters. - DBS: Dinucleotide substitution. - MNS: Multinucleotide substitution. - SNV: Single nucleotide variant. - ID: Small insertions and deletions.

For more details, refer to the Output - vcf_files page.

Plots

This output folder contains the generated plots from the results of the SBS, DBS, and ID matrix generation.

For more details, refer to the Output - Plots page.