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Created with Raphaël 2.2.022Jul1Feb31Jan292522181028Nov1918May17149Merge branch 'update_count_reads' into 'master'mastermasteradded a new script for counting readsupdate_count_re…update_count_readsMerge branch 'master' of ssh://git.scicore.unibas.ch:2222/AnnotationPipelines/riboseq_pipelineAddition of output files in finish rule of process_data SnakefileUpdate README.mdUpdate README.mdUpdate README.mdAdd README.mdChange script that counts oligos. Fix wrongly replaced annotation in config files.Many changes: count of oligos, identification of overrepresented sequences, trimming of bases in the beginning in case of the smarter-kit protocol.Fixed typo in the rule read_length_histogram that caused crashing the pipeline.Small change in Snakefile. Change in config.yaml to include more files.Removed cluster_log from Snakefile. Altered run_snakefile.sh. Removed unecessary generation of directories in Snakefile of process_data.Updated run_snakefile.shRemoved cluster_log from rules in prepare_annotation Snakefile. Removed create directories rule in prepare_annotation Snakefile. Altered cluster.json in prepare_annotation Snakefile. Removed unecessary info from config.yaml in prepare_annotation Snakefile.Creation of bed file for the CDS coordinatesAddition of script that filters reads based on P-site offsets and read length and creates the A-site coverage.Addition of scripts that determines the p-site offset based on different read lengthsAddition of scripts that couts the number of reads in the CDS in the process data pipeline.Addition of script that plots the creates a read length histogram based on the mapped reads in the process data pipeline.Addition of rule that removes multimappers in the process data pipelineAddition of create_tab_delimited_CDS_file.py in the prepare annotation pipeline. Added perl script for counting riboseq reads. Needs to be further added in the process data pipeline.Update SnakefileSmall changesChanges in process data pipelineAddition of prepare_annotation pipeline. Small changes in process_data pipeline.Update .gitignoreAdded mapping steps in snakemake process_data pipelineFirst commit