Page Comparison

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• mapreads_interpreter: Converts a mapreads output file into a tab-delimited info file.
  • Inputs: mapreads output file; reference fasta file
    Outputs: Info file with readid\tgi#\tmismatches\tdirection\tstartlocation\tstart%\tend%\tcoverage%\tgenedescription\tgenelength
• mapreads_interpreter_SREK: Converts a SREK mapping output file into a tab-delimited info file.
  • Inputs: SREK output file (after extension); reference fasta file
    Outputs: Info file with readid\tgi#\tmismatches\tdirection\tstartlocation\tstart%\tend%\tcoverage%\tgenedescription\tgenelength\tfragmentlength* mapreads_select_mismatches: Will filter info file by number of mismatches
  • Inputs: info file generated by mapreads_interepreter; mismatch cutoff
    Outputs: info file filtered to include only mappings with mismatches less than or equal to user specified cutoff* mapreads_select_by_length: Will filter info filter by length
  • Inputs: info file generated by mapreads_interpreter_SREK; minimum length; maximum length
    Outputs: info file filtered to include only results with mapping length within user specified cutoff

Bowtie related parsers

• bowtie_interpreter: Converts a bowtie mapping output file into a tab-delimited info file.
  • Inputs: bowtie output file; reference fasta file
    Outputs: Info file with readid\tgi#\tdirection\tmismatches\tstart%\tend%\tcoverage%\tgenedescription\tgenelength; start locations for each mapping
• bowtie_select_mismatches: Will filter info file by number of mismatches
  • Inputs: info file generated by bowtie; mismatch cutoff
    Outputs: info file filtered to include only mappings with mismatches less than or equal to user specified cutoff* bowtie_filter_all_repeats: Will filter the bowtie mapping output file to exclude poly-N reads (within a limit set by the user).
  • Inputs: bowtie output file; poly-N limit (a read with poly-N regions longer than or equal to the limit are excluded).
    Outputs: filtered bowtie output file.