CRISPRessoAggregate Examples

Example:

Using Bioconda:

CRISPRessoAggregate --name "VEGFA" --prefix CRISPRessoRuns/VEGFA/

Using Docker:

docker run -v ${PWD}:/DATA -w /DATA -i pinellolab/crispresso2 CRISPRessoAggregate --name "VEGFA" --prefix CRISPRessoRuns/VEGFA/

The output will consist of:

  1. CRISPResso2Aggregate_report.html: a html file containing links to all aggregated runs.
  2. CRISPRessoAggregate_amplicon_information.txt: A tab-separated file with a line for each amplicon that was found in any run. The 'Amplicon Name' column shows the unique name for this amplicon sequence. 'Number of sources' shows how many runs the amplicon was found in, and 'Amplicon sources' show which run folders the amplicon was found in, as well as the name of the amplicon in that run.
  3. CRISPRessoAggregate_mapping_statistics.txt: A tab-separated file showing the number of reads sequenced and mapped for each run.
  4. CRISPRessoAggregate_quantification_of_editing_frequency.txt: A tab-separated with the number of reads and edits for each run folder. Data from run folders with multiple amplicons show the sum totals for all amplicons.
  5. CRISPRessoAggregate_quantification_of_editing_frequency_by_amplicon.txt: A tab-separated file showing the number of reads and edits for each amplicon for each run folder. Data from run folders with multiple amplicons will appear on multiple lines, with one line per amplicon.