comparison htseq-count.xml @ 6:08a11d1eaec6

Updated HTSEQ package to version 0.5.4p1, attempted to fix galaxy install where lib64 directory does not exist

5:0a835934d792

<tool id="htseq_count" name="htseq-count" version="0.3">
    <description> - Count aligned reads in a BAM file that overlap features in a GFF file</description>
    <version_command>htseq-count -h | grep version | sed 's/^\(.*\)*\(version .*\)\./\2/'</version_command>
    <requirements>
        <requirement type="package" version="1.6.2">numpy</requirement>
        <requirement type="package" version="0.5.3p9">htseq</requirement>
        <requirement type="package" version="0.1.18">samtools</requirement>
        <requirement type="package" version="1.56.0">picard</requirement> 
    </requirements>
    <command>
    ##set up input files

each gene is considered here as the union of all its exons. One may also consider 
each exon as a feature, e.g., in order to check for alternative splicing. For 
comparative ChIP-Seq, the features might be binding regions from a pre-determined 
list.

**Paired-end Data MUST be sorted by QUERY NAME first**

This tool requires that paired-end data be sorted by query name, which is NOT the default for Galaxy. Using the Picard Paired Read Mate Fixer with Query name sort FIRST is required for paired end data.


Overlap Modes
-------------

Special care must be taken to decide how to deal with reads that overlap more than one feature. 

The following figure illustrates the effect of these three modes:

.. image:: /static/images/count_modes.png
    :width: 500

Strandedness
------------

**Important**: The default for strandedness is yes. If your RNA-Seq data has not been made with a strand-specific protocol, this causes half of the reads to be lost. Hence, make sure to set the option Stranded to 'No' unless you have strand-specific data!

Output
------

The script outputs a table with counts for each feature, followed by the special counters, which count reads that were not counted for any feature for various reasons, namely

6:08a11d1eaec6

<tool id="htseq_count" name="htseq-count" version="0.3.1">
    <description> - Count aligned reads in a BAM file that overlap features in a GFF file</description>
    <version_command>htseq-count -h | grep version | sed 's/^\(.*\)*\(version .*\)\./\2/'</version_command>
    <requirements>
        <requirement type="package" version="1.6.2">numpy</requirement>
        <requirement type="package" version="0.5.4p1">htseq</requirement>
        <requirement type="package" version="0.1.18">samtools</requirement>
        <requirement type="package" version="1.56.0">picard</requirement> 
    </requirements>
    <command>
    ##set up input files

each gene is considered here as the union of all its exons. One may also consider 
each exon as a feature, e.g., in order to check for alternative splicing. For 
comparative ChIP-Seq, the features might be binding regions from a pre-determined 
list.


Overlap Modes
-------------

Special care must be taken to decide how to deal with reads that overlap more than one feature. 

The following figure illustrates the effect of these three modes:

.. image:: /static/images/count_modes.png
    :width: 500


Strandedness
------------

**Important**: The default for strandedness is yes. If your RNA-Seq data has not been made with a strand-specific protocol, this causes half of the reads to be lost. Hence, make sure to set the option Stranded to 'No' unless you have strand-specific data!


Output
------

The script outputs a table with counts for each feature, followed by the special counters, which count reads that were not counted for any feature for various reasons, namely