bamPEFragmentSize (version 3.5.4+galaxy0)

Sample order matters:

By default, the order of samples given to the program is dependent on their order in your history. If the order of the samples is vital to you, select Yes below.

BAM/CRAM file:

Would you like custom sample labels?:

By default, the names of the samples in your history are used.

Get the distribution of read/fragment lengths as a histogram:

Image file format:

Note that the plotly output can be very large and not all options are supported.

Labels for the samples (each BAM file) 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 itself contains a space E.g. label-1 "label 2"

Title of the plot:

Title of the plot, to be printed on top of the generated image.

Show advanced options:

What it does

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.

Output

The default output is a simple summary statistic for the observed fragment lengths.

Optionally, you can obtain a histogram of fragment sizes, which will give you a better idea of the distribution of fragment lengths.

/repository/static/images/af23ee74c7315b8f/bamPEFragmentSize_output.png

If the --table option is specified, the summary statistics are additionally printed in a tabular format:

    Frag. Len. Min. Frag. Len. 1st. Qu.     Frag. Len. Mean Frag. Len. Median       Frag. Len. 3rd Qu.      Frag. Len. Max  Frag. Len. Std. Read Len. Min.  Read Len. 1st. Qu.      Read Len. Mean  Read Len. Median        Read Len. 3rd Qu.       Read Len. Max   Read Len. Std.
bowtie2 test1.bam   241.0   241.5   244.666666667   242.0   246.5   251.0   4.49691252108   251.0   251.0   251.0   251.0   251.0   251.0   0.0

If the --outRawFragmentLengths option is provided, another history item will be produced, containing the raw data underlying the histogram. It has the following format:

#bamPEFragmentSize
Size        Occurrences     Sample
241 1       bowtie2 test1.bam
242 1       bowtie2 test1.bam
251 1       bowtie2 test1.bam

The "Size" is the fragment (or read, for single-end datasets) size and "Occurrences" are the number of times reads/fragments with that length were observed. For easing downstream processing, the sample name is also included on each row.

For more information on the tools, please visit our help site.

For support or questions please post to Biostars. For bug reports and feature requests please open an issue on github.

This tool is developed by the Bioinformatics and Deep-Sequencing Unit at the Max Planck Institute for Immunobiology and Epigenetics.