SCALPEL (SCRibo-seq analysis pipeline)

latest version: 0.2 (12.04.2021)

The scripts provided in this repository can be used to manipulate data from SCRibo-Seq experiments using the NextSnakes pipeline. The necessary configurations to process the SCRibo-Seq data are explained in detail there.

Quantification of ribozyme annotation sites in species' genomes

After running cmsearch to find ribozyme annotation sites (included in the NextSnakes pipelines), cmsearch output files can be analyzed with cmsearch_analysis.sh. the script gives results for single ribozyme types. The bed files for each investigated CM should be copied or linked to one directory.

sh cmsearch_analysis.sh PATHTORIBOBEDFILEDIRECTORY E-VALUETHRESHOLDFORHITS

Count, length, and e-values of annotation sites under the given threshold are saved in several tab-separated csv files. Additionally, visualisations are provided in the cmsearch_plots directory.

Quantification of ribozyme peaks from Ribozeq experiments

To analyze peaks from SCRibo-seq experiments, link or copy peak files from peak finding to the directory "peaks". Then run the following script:

sh peak_analysis.sh PATHTORIBOZYMEANNOTATION

sh peak_analysis_other.sh PATHTORIBOZYMEANNOTATION PATHTOGENOMEANNOTATION

In case of clustering of the ribozyme sequences, run the following script:

sh peak_analysis_cluster.sh PATHTOCLUSTERFILE sh peak_analysis_other.sh PATHTOCLUSTERFILE PATHTOGENOMEANNOTATION

Frequenz of either ribozyme or other peaks are saved in several tab-separated csv files. Additionally, visualisations are given in the plots directory.