Reference Code backup Executable files
This tool samples the given BAM files with paired-end data to estimate the fragment length distribution. Properly paired reads are preferred for computation, i.e., unless a region does not contain any concordant pairs, discordant pairs are ignored.
bamPEFragmentSize [-h] [--bamfiles bam files [bam files ...]] [--histogram FILE] [--plotFileFormat FILETYPE] [--numberOfProcessors INT] [--samplesLabel SAMPLESLABEL [SAMPLESLABEL ...]] [--plotTitle PLOTTITLE] [--maxFragmentLength MAXFRAGMENTLENGTH] [--logScale] [--binSize INT] [--distanceBetweenBins INT] [--blackListFileName BED file] [--table FILE] [--outRawFragmentLengths FILE] [--verbose] [--version]
bamPEFragmentSize is a tool from the deepTools suite. The information on this page is based on deepTools version 3.5.1.
–bamfiles, -b List of BAM files to process
–histogram, -hist Save a .png file with a histogram of the fragment length distribution.
–numberOfProcessors, -p Number of processors to use. The default is to use 1.
–samplesLabel Labels for the samples plotted. The default is to use the file name of the sample. The sample labels should be separated by spaces and quoted if a label itselfcontains a space E.g. –samplesLabel label-1 “label 2”
–plotTitle, -T Title of the plot, to be printed on top of the generated image. Leave blank for no title.
–maxFragmentLength The maximum fragment length in the histogram. A value of 0 (the default) indicates to use twice the mean fragment length
–logScale Plot on the log scale
–binSize, -bs Length in bases of the window used to sample the genome. (default 1000)
–distanceBetweenBins, -n To reduce the computation time, not every possible genomic bin is sampled. This option allows you to set the distance between bins actually sampled from. Larger numbers are sufficient for high coverage samples, while smaller values are useful for lower coverage samples. Note that if you specify a value that results in too few (<1000) reads sampled, the value will be decreased. (default 1000000)
–blackListFileName, -bl A BED file containing regions that should be excluded from all analyses. Currently this works by rejecting genomic chunks that happen to overlap an entry. Consequently, for BAM files, if a read partially overlaps a blacklisted region or a fragment spans over it, then the read/fragment might still be considered.
–verbose Set if processing data messages are wanted.
–version show program’s version number and exit