The tool works with sequencing reads from the Illumina Platform in FASTQ or fastq.gz format. Multiple FASTQ files can be zipped as either tar.gz or .zip and can be uploaded into the tool.
Single-end or Paired-end sequences are suitable.
Human, mouse and rat genome references are available.
Narrow peak or broad peak options are available with the data analysis tool.
Sequence data (raw read) QC is done by using the FastQC quality check tool. This tool has been widely used in various publications and has greater acceptance in the scientific community for FASTQ file quality check. The quality check is based on the sequence quality of the individual bases in the reads and the reports are generated accordingly. For more details, please refer to https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
It is recommended to use narrow peak for the identification of transcription factor binding locations and broad peak for the investigation of histone modification.
Both un-barcoded and barcoded samples can be analyzed using the data analysis tool. Select either “Un-Barcoded samples” or “Barcoded samples” in the “Peak call & annotation” page.
Both single sample or multiple replicates workflows are designed and configured in the tool. Customers can choose either workflow to complete the data analysis.
Depending on your samples (e.g. single or multiple replicates) and choice of analyses, several reports can be generated and are available for download, including:
For customers who purchased our ChIC/CUT&RUN kits, they can access the data analysis tool for free by following the steps in the instruction sheet found in the ChIC/CUT&RUN kit’s package. An overview of the data analysis tool can be viewed here.
To obtain access to the ChIC/CUT&RUN data analysis tool, please click here. Your order ID can be found on the packing slip, the order confirmation or retrieved by calling your local Customer Service.
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