Python package to find chimeras in CRAC/CLASH and HITS-CLIP datasets
Project description
Introduction
CLASHChimeras is a Python package for analysing CLASH datasets. It takes raw fastq files as input and provides comprehensive analysis of RNA profiles and chimeric reads identification. The output is CSV and BED format files for easy visualization in Genome Browsers.
Dependencies
CLASHChimeras requires certain software to be installed and setup before you can use it completely. The software you need to explicitly install are the following:
Usage
The package can be used by three executable scripts
download-for-chimeras
download-for-chimeras -gr latest -mr latest -gor "H.sapiens" -mor hsaDownloads required sequences and create bowtie2 indexes required for alignment
align-for-chimeras
align-for-chimeras -i input.fastq -pa /path/to/database -o outputGiven a fastq file, this script executes bowtie2 and tophat aligners to generate alignment files necessary for detecting chimeras in the reads
find-chimeras
find-chimeras -s smallRNA.sam -t targetRNA.sam -o outputGiven two SAM files, this script tries to find chimeras that are observed between a smallRNA and a targetRNA
Check out the documentation for detailed usage and installation instructions
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