comparison bamCompare.xml @ 28:f7712a057440 draft

new bugfix release

27:bf1b1dcdd67b

<tool id="deeptools_bamCompare" name="bamCompare" version="1.0.5">
    <description>normalizes and compares two BAM files to obtain the ratio, log2ratio or difference. (bam2bigwig)</description>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <macros>
        <token name="@BINARY@">bamCompare</token>

    <help>

**What it does**

This tool compares two BAM files based on the number of mapped reads. To
compare the BAM files, the genome is partitioned into bins of equal size,
the reads are counted for each bin and each BAM file and finally, a summarizing value is reported.
This value can be the ratio of the number of reads per bin, the log2 of the ratio or the difference.
This tool can normalize the number of reads on each BAM file using the SES method
proposed by Diaz et al. (2012). Stat Appl Genet Mol Biol 11(3). Normalization based on read counts is also available. The
output is either a bedGraph or a bigWig file containing the bin location and
the resulting comparison values.
If paired-end reads are present, the fragment
length reported in the BAM file is used by default.


.. image:: $PATH_TO_IMAGES/norm_IGVsnapshot_indFiles.png

28:f7712a057440

<tool id="deeptools_bamCompare" name="bamCompare" version="@WRAPPER_VERSION@.0">
    <description>normalizes and compares two BAM files to obtain the ratio, log2ratio or difference. (bam2bigwig)</description>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <macros>
        <token name="@BINARY@">bamCompare</token>

    <help>

**What it does**

This tool compares two BAM files based on the number of mapped reads. To
compare the BAM files, the genome is partitioned into bins of equal size, then
the number of reads found in each BAM file is counted for such bins and
finally a summarizing value is reported. This value can be the ratio of the
number of reads per bin, the log2 of the ratio or the difference. This tool
can normalize the number of reads on each BAM file using the SES method
proposed by Diaz et al. (2012). "Normalization, bias correction, and peak
calling for ChIP-seq". Statistical applications in genetics and molecular
biology, 11(3). Normalization based on read counts is also available. The
output is either a bedgraph or a bigwig file containing the bin location and
the resulting comparison values. By default, if reads are mated, the fragment
length reported in the BAM file is used. In the case of paired-end mapping
each read mate is treated independently to avoid a bias when a mixture of
concordant and discordant pairs is present. This means that *each end* will be
extended to match the fragment length.


.. image:: $PATH_TO_IMAGES/norm_IGVsnapshot_indFiles.png