tsjzz / mazter_mine

An R program to calculate cleavage efficiency in MAZTER-seq derived data

MAZTER-mine

Citation

If you use this code, please cite it as: Miguel Angel García-Campos. (2019, December 17). SchwartzLab/mazter_mine: Minor update (Version v1.0.1). Cell. Zenodo. http://doi.org/10.5281/zenodo.3581426

Description

MAZTER-mine is a computational pipeline to analyze MAZTER-seq (Garcia-Campos et al., 2019) derived data, a methodology that profiles m6A quantitatively across transcriptomes with a single-base resolution.

This repository holds two programs to run the MAZTER-seq computational pipeline, a set of helper functions, and an additional folder which includes a tutorial and test data to run it:

helperFunctions.R

An R script with helper functions. For an easier handling this functions are loaded from the online repository when running bam2ReadEnds.R and mazter_seq.R. If you want to run these while offline, please change the path in the source() function at the beginning of the main programs to your local copy of "helperFunctions.R".

bam2ReadEnds.R

This is an R script that should be used as a command line tool in a UNIX system, providing the necessary arguments.

e.g. Rscript bam2ReadEnds.R -i Sample1.bam -g geneAnnot.bed

Its main input is an unsorted alignment file in BAM format and a gene annotation in BED-12 format. This processing step may be lengthy, depending on computational power and file size.

Rscript bam2ReadEnds.R --help

Usage: bam2ReadEnds.R [options]

Options:
        -i CHARACTER, --BAMfile=CHARACTER
                UNSORTED_BAM alignment file

        -g CHARACTER, --geneAnnotation=CHARACTER
                Gene annotation file in BED-12 format

        -l NUMERIC, --maxInsLen=NUMERIC
                Maximum mapped insert length [default= 200]

        -m NUMERIC, --minInsG=NUMERIC
                Minimum number of inserts to report gene [default= 15]

        -n NUMERIC, --nCores=NUMERIC
                Number of cores to be used [default= 2]

        -h, --help
                Show this help message and exit

mazter_mine.R

This is a program that should be used as a command line tool in a UNIX system, providing the necessary arguments.

mazter_mine's main input is the ".Rdata" file output from the bam2ReadEnds.R program, and it outputs a QC report and a cleavage efficiency table which can be used for downstream statistical analysis.

Rscript master_mine.R --help
Usage: master_mine.R [options]


Options:
        -i CHARACTER, --countDataFile=CHARACTER
                .Rdata file with count data (bam2readEnds.R output)

        -g CHARACTER, --geneAnnotation=CHARACTER
                Gene annotation file in BED-12 format

        -f CHARACTER, --faGenome=CHARACTER
                FASTA genome file to retrieve gene seqs

        -c CHARACTER, --clvMotif=CHARACTER
                Cleavage motif to measure at [default= ACA]

        -m NUMERIC, --minCov=NUMERIC
                Minimum coverage to quantify site [default= 15]

        -u NUMERIC, --upSThr=NUMERIC
                Up-stream distance to closest motif threshold

        -d NUMERIC, --doSThr=NUMERIC
                Down-stream distance to closest motif threshold

        -n NUMERIC, --nCores=NUMERIC
                Number of cores to be used [default= 2]

        -t CHARACTER, --tagName=CHARACTER
                Tag used for output files naming

        -h, --help
                Show this help message and exit

tutorial

An example MAZTER-mine run with test data.

Dependencies:

• Bedtools (tested using samtools 1.3.1)
• SAMtools (tested using bedtools 2.26.0)