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PacificBiosciences / kineticsTools

Tools for detecting DNA modifications from single molecule, real-time sequencing data
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summarizeModifications Input Question #61

Open JohnUrban opened 5 years ago

JohnUrban commented 5 years ago

Hi,

I want to see what "summarizeModifications" outputs, but I am not familiar with one of its input requirements.

Specifically how do I generate the alignmentSummary GFF requested here:

$ summarizeModifications -h
usage: summarizeModifications [-h] [--version] [--emit-tool-contract]
                              [--resolved-tool-contract RESOLVED_TOOL_CONTRACT]
                              [--log-file LOG_FILE]
                              [--log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL} | --debug | --quiet | -v]
                              modifications alignmentSummary gff_out

Summarizes kinetic modifications in the alignment_summary.gff file.

positional arguments:
  modifications         Base modification GFF file
  alignmentSummary      Alignment summary GFF
  gff_out               Coverage summary for regions (bins) spanning the
                        reference with basemod results for each region

Many thanks,

John