CRISPRessoBatch Examples

Example run: Batch mode

Download the test dataset files SRR3305543.fastq.gz, SRR3305544.fastq.gz, SRR3305545.fastq.gz, and SRR3305546.fastq.gz to your current directory. These are files are the first 25,000 sequences from an editing experiment performed on several base editors. Also include a batch file that lists these files and the sample names: batch.batch To analyze this experiment, run the following command:

Using Bioconda:

CRISPRessoBatch --batch_settings batch.batch --amplicon_seq CATTGCAGAGAGGCGTATCATTTCGCGGATGTTCCAATCAGTACGCAGAGAGTCGCCGTCTCCAAGGTGAAAGCGGAAGTAGGGCCTTCGCGCACCTCATGGAATCCCTTCTGCAGCACCTGGATCGCTTTTCCGAGCTTCTGGCGGTCTCAAGCACTACCTACGTCAGCACCTGGGACCCC -p 4 --base_editor_output -g GGAATCCCTTCTGCAGCACC -wc -10 -w 20

Using Docker:

docker run -v ${PWD}:/DATA -w /DATA -i pinellolab/crispresso2 CRISPRessoBatch --batch_settings batch.batch --amplicon_seq CATTGCAGAGAGGCGTATCATTTCGCGGATGTTCCAATCAGTACGCAGAGAGTCGCCGTCTCCAAGGTGAAAGCGGAAGTAGGGCCTTCGCGCACCTCATGGAATCCCTTCTGCAGCACCTGGATCGCTTTTCCGAGCTTCTGGCGGTCTCAAGCACTACCTACGTCAGCACCTGGGACCCC -p 4 --base_editor_output -g GGAATCCCTTCTGCAGCACC -wc -10 -w 20

This should produce a folder called CRISPRessoBatch_on_batch. Open the file called CRISPRessoBatch_on_batch/CRISPResso2Batch_report.html in a web browser, and you should see an output like this: CRISPResso2Batch_report.html.