pegi3s/bedtools repository overview

⁠This image belongs to a larger project called Bioinformatics Docker Images Project (http://pegi3s.github.io/dockerfiles⁠)

⁠(Please note that the original software licenses still apply)

This image allows the usage of the Bedtools⁠ suite - a fast and flexible toolset for genome arithmetic. Bedtools allows to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF.

By running the command docker run --rm -v /your/data/dir:/data pegi3s/bedtools bedtools -h you can list the tools included in this suite, namely:

• annotateBed: annotate coverage of features from multiple files.
• bamToBed: convert BAM alignments to BED (& other) formats.
• bamToFastq: convert BAM records to FASTQ records.
• bed12ToBed6: breaks BED12 intervals into discrete BED6 intervals.
• bedToBam: convert intervals to BAM records.
• bedToIgv: create an IGV snapshot batch script.
• bedpeToBam: convert BEDPE intervals to BAM records.
• bedtools: print help menu.
• closestBed: find the closest, potentially non-overlapping interval.
• clusterBed: cluster (but don’t merge) overlapping/nearby intervals.
• complementBed: extract intervals not represented by an interval file.
• coverageBed: compute the coverage over defined intervals.
• expandCols: replicate lines based on lists of values in columns.
• fastaFromBed: use intervals to extract sequences from a FASTA file.
• flankBed: create new intervals from the flanks of existing intervals.
• genomeCoverageBed: compute the coverage over an entire genome.
• getOverlap: computes the amount of overlap from two intervals.
• groupBy: group by common cols. & summarize oth. cols. (~ SQL “groupBy”)
• intersectBed: find overlapping intervals in various ways.
• linksBed: create a HTML page of links to UCSC locations.
• mapBed: apply a function to a column for each overlapping interval.
• maskFastaFromBed: use intervals to mask sequences from a FASTA file.
• mergeBed: combine overlapping/nearby intervals into a single interval.
• multiBamCov: counts coverage from multiple BAMs at specific intervals.
• multiIntersectBed: identifies common intervals among multiple interval files.
• nucBed: profile the nucleotide content of intervals in a FASTA file.
• pairToBed: find pairs that overlap intervals in various ways.
• pairToPair: find pairs that overlap other pairs in various ways.
• randomBed: generate random intervals in a genome.
• shiftBed: adjust the position of intervals.
• shuffleBed: randomly redistribute intervals in a genome.
• slopBed: adjust the size of intervals.
• sortBed: order the intervals in a file.
• subtractBed: remove intervals based on overlaps b/w two files.
• tagBam: tag BAM alignments based on overlaps with interval files.
• unionBedGraphs: combines coverage intervals from multiple BEDGRAPH files.
• windowBed: find overlapping intervals within a window around an interval.
• windowMaker: make interval “windows” across a genome.

Note: You may notice some mismatches between the tools names shown in the help list and the names of the corresponding executable functions. Check it please, by performing:

docker run -it pegi3s/bedtools
ls /opt/bedtools2/bin/

In case the mismatch happens, you should use the names of the executable functions.

To obtain the help of a particular application, you just need to run: docker run --rm -v /your/data/dir:/data pegi3s/bedtools <bedtools-application-name> (e.g. docker run --rm -v /your/data/dir:/data pegi3s/bedtools fastaFromBed)

⁠Using the Bedtools image in Linux

To run an application, you should adapt and run the following command: docker run --rm -v /your/data/dir:/data pegi3s/bedtools <bedtools-application-name> -fi <input FASTA> -bed <BED/GFF/VCF> -fo /data/stdout

In this command, you should replace:

• /your/data/dir to point to the directory that contains the input files you want to analyze.
• <bedtools-application-name> to the name of the Bedtools application you want to use.
• <input FASTA> to the actual name of your input FASTA file.
• <BED/GFF/VCF> to the actual name of your input BED/GFF/VCF file.
• stdout to the actual name of your output file.

For instance, to use the fastaFromBed application, you should run: docker run --rm -v /your/data/dir:/data pegi3s/bedtools fastaFromBed -fi /data/input_fasta -bed /data/input_gff -fo /data/stdout

Note: In order to use a less complex BED/GFF/VCF file you may want to filter it for exons first, for example, by performing:

grep -P "\texon\t" input_gff