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comparison htseq.xml @ 8:734516a21b52 draft

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author fcaramia
date Thu, 13 Sep 2012 00:51:13 -0400
parents a535c6d80fb0
children 17983775f1b0
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7:3aadcea3347b 8:734516a21b52
1 <tool id="htseq-count" name="Count reads in features with htseq-count" version="1.0.0"> 1 <tool id="htseq-count" name="Count reads in features with htseq-count" version="1.0.0">
2 2 <description> - Create a digital expression matrix by counting reads in features with htseq-count</description>
3 <command interpreter="perl"> 3 <command interpreter="perl">
4 htseq.pl -m $MODE -s $STRANDED -a $MINAQUAL -t $FEATURETYPE -i $IDATTR -g $gff_file -o $output -r $report $REDUCE 4 htseq.pl -m $MODE -s $STRANDED -a $MINAQUAL -t $FEATURETYPE -i $IDATTR -g $gff_file -o $output -r $report $REDUCE
5 ## Inputs. 5 ## Inputs.
6 #for $group in $group_analysis 6 #for $group in $group_analysis
7 ${group.group}::${group.sample_init}::${group.file_init} 7 ${group.group}::${group.sample_init}::${group.file_init}
68 68
69 If S contains precisely one feature, the read is counted for this feature. If it contains more than one feature, the read is counted as ambiguous (and not counted for any features), and if S is empty, the read is counted as no_feature. 69 If S contains precisely one feature, the read is counted for this feature. If it contains more than one feature, the read is counted as ambiguous (and not counted for any features), and if S is empty, the read is counted as no_feature.
70 70
71 The following figure illustrates the effect of these three modes: 71 The following figure illustrates the effect of these three modes:
72 72
73 .. image:: ./static/operation_icons/count_modes.png 73 .. image:: http://www-huber.embl.de/users/anders/HTSeq/doc/_images/count_modes.png
74 74
75 The strandedness of the assay may also be set. For stranded=no, a read is considered overlapping with a feature regardless of whether it is mapped to the same or the opposite strand as the feature. For stranded=yes and single-end reads, the read has to be mapped to the same strand as the feature. For paired-end reads, the first read has to be on the same strand and the second read on the opposite strand. For stranded=reverse, these rules are reversed. 75 The strandedness of the assay may also be set. For stranded=no, a read is considered overlapping with a feature regardless of whether it is mapped to the same or the opposite strand as the feature. For stranded=yes and single-end reads, the read has to be mapped to the same strand as the feature. For paired-end reads, the first read has to be on the same strand and the second read on the opposite strand. For stranded=reverse, these rules are reversed.
76 76
77 .. class:: warningmark 77 .. class:: warningmark
78 78
88 * ambiguous: reads which could have been assigned to more than one feature and hence were not counted for any of these (set S had more than one element). 88 * ambiguous: reads which could have been assigned to more than one feature and hence were not counted for any of these (set S had more than one element).
89 * too_low_aQual: reads which were not counted due to the -a option, see below 89 * too_low_aQual: reads which were not counted due to the -a option, see below
90 * not_aligned: reads in the Sam/Bam file without alignment 90 * not_aligned: reads in the Sam/Bam file without alignment
91 * alignment_not_unique: reads with more than one reported alignment. These reads are recognized from the NH optional SAM field tag. (If the aligner does not set this field, multiply aligned reads will be counted multiple times.) 91 * alignment_not_unique: reads with more than one reported alignment. These reads are recognized from the NH optional SAM field tag. (If the aligner does not set this field, multiply aligned reads will be counted multiple times.)
92 92
93 **Reference**
94
95 http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html
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97
98
93 </help> 99 </help>
94 100
95 </tool> 101 </tool>