Table: Count mutations for each read and position

Table: Input files

Table input file: Report

You can give any number of report files from the Relate, Mask, and Cluster steps as inputs for the Table step. See List Input Files for ways to list multiple files.

To tabulate all results in {out}, you can use the command

seismic table {out}

Table: Settings

Table setting: Suppress per-position and per-read tables

SEISMIC-RNA outputs all possible tables by default. To suppress per-position and per-read tables, use --no-table-pos and --no-table-read, respectively.

Table: Output files

All output files go into the directory {out}/{sample}/table/{ref}/{sect}, where {out} is the output directory, {sample} is the sample, {ref} is the reference, and {sect} is the section. Each output file from Relate, Mask, and Cluster reports are prefixed with relate-, mask-, and clust-, respectively.

Table output file: Relationships per position

SEISMIC-RNA outputs the number of relationships at each position to a CSV file named {step}-per-pos.csv, where {step} is relate/mask/clust.

Table output file: Relationships per read

SEISMIC-RNA outputs the number of relationships in each read to a CSV file named {step}-per-read.csv.gz, where {step} is relate/mask/clust.

Table output file: Reads per cluster

For Cluster reports, SEISMIC-RNA outputs the number of reads in each cluster to a CSV file named clust-freq.csv.