bamPEFragmentSize

This tool calculates the fragment sizes for read pairs given a BAM file from paired-end sequencing.Several regions are sampled depending on the size of the genome and number of processors to estimate thesummary statistics on the fragment lengths. Properly paired reads are preferred for computation, i.e., it will only use discordant pairs if no concordant alignments overlap with a given region. The default setting simply prints the summary statistics to the screen.

usage: bamPEFragmentSize [-h] [--histogram FILE] [--numberOfProcessors INT]
                         [--plotTitle PLOTTITLE] [--binSize INT]
                         [--distanceBetweenBins INT]
                         [--blackListFileName BED file] [--verbose]
                         [--version]
                         bam-file

Positional arguments:

bam	BAM file to process

optional arguments

--histogram, -hist
	Save a .png file with a histogram of the fragment length distribution.
--numberOfProcessors=1, -p=1
	Number of processors to use. The default is to use 1.
--plotTitle=, -T=
	Title of the plot, to be printed on top of the generated image. Leave blank for no title.
--binSize=1000, -bs=1000
	Length in bases of the window used to sample the genome. (default 1000)
--distanceBetweenBins=1000000, -n=1000000
	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=False
	Set if processing data messages are wanted.
--version	show program’s version number and exit

Note

This tool accepts only one BAM file at a time.

Example usage

$ deepTools2.0/bin/bamPEFragmentSize \
-hist fragmentSize.png \
-T "Fragment size of PE RNA-seq data" \
testFiles/RNAseq.bam

 Sample size: 12850

Fragment lengths:
    Min.: 0.0
    1st Qu.: 313.0
    Mean: 2597.03237354
    Median: 357.0
    3rd Qu.: 2726.0
    Max.: 384622.0
    Std: 7066.11863701

Read lengths:
    Min.: 20.0
    1st Qu.: 101.0
    Mean: 99.4182101167
    Median: 101.0
    3rd Qu.: 101.0
    Max.: 101.0
    Std: 7.64455778462

deepTools Galaxy.

code @ github.